General information for g12952.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as NPC intracellular cholesterol transporter 1.
Parent gene
- The parent gene g12952 is located on chr_1: 27111772..27114877 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g12952 | g12952.t1 | isoform | g12952.t1 | 27108335 | 27114877 |
| chr_1 | g12952 | g12952.t1 | exon | g12952.t1.exon1 | 27108335 | 27108429 |
| chr_1 | g12952 | g12952.t1 | cds | g12952.t1.CDS1 | 27108335 | 27108429 |
| chr_1 | g12952 | g12952.t1 | exon | g12952.t1.exon2 | 27108482 | 27109366 |
| chr_1 | g12952 | g12952.t1 | cds | g12952.t1.CDS2 | 27108482 | 27109366 |
| chr_1 | g12952 | g12952.t1 | exon | g12952.t1.exon3 | 27109557 | 27111383 |
| chr_1 | g12952 | g12952.t1 | cds | g12952.t1.CDS3 | 27109557 | 27111383 |
| chr_1 | g12952 | g12952.t1 | exon | g12952.t1.exon4 | 27111446 | 27111770 |
| chr_1 | g12952 | g12952.t1 | cds | g12952.t1.CDS4 | 27111446 | 27111770 |
| chr_1 | g12952 | g12952.t1 | exon | g12952.t1.exon5 | 27112240 | 27112541 |
| chr_1 | g12952 | g12952.t1 | cds | g12952.t1.CDS5 | 27112240 | 27112541 |
| chr_1 | g12952 | g12952.t1 | exon | g12952.t1.exon6 | 27112597 | 27112756 |
| chr_1 | g12952 | g12952.t1 | cds | g12952.t1.CDS6 | 27112597 | 27112756 |
| chr_1 | g12952 | g12952.t1 | exon | g12952.t1.exon7 | 27112854 | 27113087 |
| chr_1 | g12952 | g12952.t1 | cds | g12952.t1.CDS7 | 27112854 | 27113087 |
| chr_1 | g12952 | g12952.t1 | exon | g12952.t1.exon8 | 27114830 | 27114877 |
| chr_1 | g12952 | g12952.t1 | cds | g12952.t1.CDS8 | 27114830 | 27114877 |
| chr_1 | g12952 | g12952.t1 | TSS | g12952.t1 | 27115022 | 27115022 |
| chr_1 | g12952 | g12952.t1 | TTS | g12952.t1 | NA | NA |
Sequences
>g12952.t1 Gene=g12952 Length=3876
ATGTGCAAGTTGCAATTAAGATTACTTAAATTACTGTTGCTAATTGTGACAACATTGCTT
GGTCAAAGGTTAGTGAAATGTGATGTGAAGCAAAGTAATAGTTGTGTGTGGTATGGAATT
TGTGATCGAGTTAAGGAGTACAATTCAGTGAAAATTAAAAATTGTGCTTATGATGGTCCA
CCTAAAAAATTAGATTCAAATGGAGTTTTTGCATTGAATGAATGGTGCTCACATTTACGA
GAGGATGACGATGATGTTTACACTTGTTGTGATAATGAACAGCTTTATGCACTAAACGAA
AACATCAAACAAGCTTCAAATCTTCTAAATCGTTGCCCAGCTTGCATGAAAAATTTTGCA
AAACATATTTGTGATTATATTTGTAGCCCACGTCATGGTGAATTCATTAATGTTTTAAAG
AAAAAACAAAGCATATCAAAACCAAATAAAGAATATATCGATGAAATTGATTTGTTTGTT
ACTGAAGATTATTTAAATGGAACTTATGATTCTTGTAAAAATGTTTTAATGCCATCGACT
GGTCAAAAAGTGATGGATATGATGTGTGGTGGTTTTCCTGCATCAAAATGTTCACCAATG
AGATGGTTTCAACATATGGGTGATGTGAATGTCGCACAAATTCCATTTCAAATCAATTAT
ATTCCACAAAAATCATTGATGACTTCTGACAATAAATTTAAACCAATGAATCCAAAAATT
ATTCCATGCAATGAAAGTTTTAATAATGATCCACCATGTTCATGCGTCGATTGTATTTCA
TCATGTCCAATAGCACAGGAAGTAAAAAAGAATTCTGAAAACTTTAAAATTCTCAACTAT
GACGGCTATATTTTCATAATTATGCTCATATTCTTCATTGGCAGTTTAATGTTTACGGTG
TTTGCAAACAGAAAAGTTCCGAGTAAAGAAATGAATCACATAAAGAACAAGAATTTTGAA
TTGAGTATGTCAGAACAATATGCTCAAAAAGTTGAAAAGTTTTTACAGGAAATATTTACT
AATTGGGGAAAATTTTGTGCAACTCATCCATTGAAAGTTATTTTTATAAGTTTGTTATTA
GTCGCATGTTTTGCTTATGGAACACGATTTTCACAAGTAACTGTCGATCCAATTGAATTA
TGGGCTTCATCAACTTCTCAATCACGCATTCAAAAAGATTTTTTTGATTCAAAATTTGAT
CCATTTTATCGAGTTGAGCAAGTAATCATTACAGCCAAAGGTTATCAGGATATCATTCAC
AATACATCAAATGGGGTCATTAATTTTGGACCAGCTTTTAACAAAGAATTTCTTTTAAAA
GTGCTAGAAATTCAACAATCAATTGAAAATATTGACAATGGAGTTTTAAAGGACATTTGT
TTTGCACCATTAAGATCTGCAAATTTACCAAAAGATGAATATGAAGTGACTGATTGCCTT
GTACAGAGTATTTGGGGCTATTTCCAAAATAGAAAAAAAGAAATTACCGATCCAAAAAGG
AATAATAGAAAAGACAAAAATAATTTCACTGTTAATTACCTCGATACACTTTATAATTGC
TTTCAAAATCCTTTTGATACGACTTGTTTTGCAACATACAAAGGTCCAATTGATCCAGCA
GTCGCACTTGGTGGTTTCAATGAAAATAATGATACAATGCCAAAAAATCCAAAATATGAG
CGTGCAAGTTCAGTGATTCTTACTTTCTTATTAAATAACTATAATGATGATTTAAAGGTC
AAAGCTGCAAAAGAGTGGGAAGAGAAATTTGTCAAATTAATGCAAAACTACACAAGAAAT
GAAAATAATTCAATGATTGATATCGCATTTATATCAGAACGATCAATTGAAGATGAACTT
GATCGTGGTTCTAAATCAGACATTTCGACTATTATTATGTCATATTTAATAATGTTTGTC
TATATTGCTGTTGCATTAGGACATGTCAATGGCTTAAGTCGATTAATGATTGACAGTAAA
ATCACACTTGGTGTTGGGGGTGTTGTAATTGTCCTTGCATCGGTTGCAGCATCAAGTGGA
TTCTTTGGATATTGTGGAGTGTCAGCAACTTTGATAATTTTTGAAGTTGTTCCATTTTTA
GTACTTGCTGTTGGTGTCGACAATATTTTTATTCTTGTACAAACACATCAGCGTGAATCA
AGAGAAATTTCTGAAACAAATGCTGAACATATTGGAAGAATTCTTGGAAAAGTTGGACCT
TCAATTTTACTGACATCACTCAGTGAATGTACTTGTTTTTTTCTAGGTGCATTAACTGAT
ATGCCAGCTGTAAAAGCTTTTGCTTTGTATGCCGGAATGGCTTTATTATTTGATTTCCTA
TTACAAATTTCTTGCTTCGTGAGTCTTTTGGCTTTAGACACAGCACGACAAAATGAAAAT
CGATGGGATATTTTTTGCATTATTCGCGGTCCAAAGAAATCAGCTCAAATTCAAGGCAAT
AATGAAAGTGTTTTGTACAAATTCTTTAAATTTTTCTATGTTCCTTTATTAATGAAAAAG
CCAGTAAGAATTGCAGTGATAATTGTATTTTTTGGATGGCTCTGCTCAAGCATAGCTGTG
ATTTCAAAAGTTGAAGTTGGACTCGATCAAGAATTGTCAATGCCTAAAGATTCTTTTGTG
TACAAATATTTCCAACATTTAAAGAAATATTTATCAATTGGACCACCAGTTTATTTCATT
CTTAAAGGTGACCTTAATATGTCAAATACTCAAATTCAAAATATGATCTGTGGTGGAATA
AATTGCAATTTTGACAGTCTTTCAACACAAATATATTTGGCGTCGCAAGTACCTGGAAAT
ACTTATATTGCAAGACCTGCAAGCAGTTGGCTTGATGATTATTTTGATTGGTCACAATTA
CAAACATGTTGTAAACAACAAGACTCAACTAAAGAATTTTGTCCACATTCAGAAGAATTT
GATTGTCATACTTGTAACATTGTAAAGAATGAATTCAATCGACCAGTTGATAGCAATTTT
TCATATTTCATCAACTTCTTCCTACAAGATAATCCAGATGAAGATTGTGCAAAAGGTGGA
CATGCAGCATATAGCAAAGCTGTTGAAATTCTTAAGAATAATAAAATTGGTGCAAGTTAC
TTTATGAGTTACCATACAATATTAAAAACTTCTCAGGATTATTATGAAGCTCTTCGATCA
GCAAGAGAAATTTCACAAAATATCACTAAAACAATGAGAAGTAAATTACAAGAAATTGGT
CAACCAGATAATGTGGAAGTTTTTCCATATTCAGTTTTTTATGTATTTTATGAACAATAT
TTGACAATGTATCCTGACACAATTCGAAGTTTAGGAATTTCACTTCTAGCAATTTTTATC
GTCACTTTTCTGCTCATGGGCTTTGATTTTCGACTTTCATCAGTTGTCACATTAACAATT
GCTATGATTGTTATCAACATTGGAGGATTAATGTATTTTTGGAATATTTCATTAAATGCT
GTCTCTTTAGTCAATCTTGTGATGGCTGTTGGAATTTCTGTTGAATTTTGTTCACATCTT
GTGCACAGTTTTAGAGTTTCAACAAAGCATACACATTTGGAAAGAGCTGAAGATTCTTTG
ATAAAAATGGGAAGTTCAATTTTCTCAGGAATAACTTTGACTAAATTTGGTGGAATTTTT
ATTCTTGGCTTCGCACAAAGTCAAATTTTCCAAGTTTTTTACTTTAGAATGTATTTGGGA
ATTGTGCTGTATGGAGCAGCACATGGTTTGGTTTTCTTACCTGTTTTACTTACTTTTATT
GGTGGTCGCAGAAAATTAAATGACGAAAATATAGAAGATCCAGTTGAAACACCTTTAAAA
GATATGAATGAAATTGCAATAGATGAATCAAAATAA
>g12952.t1 Gene=g12952 Length=1291
MCKLQLRLLKLLLLIVTTLLGQRLVKCDVKQSNSCVWYGICDRVKEYNSVKIKNCAYDGP
PKKLDSNGVFALNEWCSHLREDDDDVYTCCDNEQLYALNENIKQASNLLNRCPACMKNFA
KHICDYICSPRHGEFINVLKKKQSISKPNKEYIDEIDLFVTEDYLNGTYDSCKNVLMPST
GQKVMDMMCGGFPASKCSPMRWFQHMGDVNVAQIPFQINYIPQKSLMTSDNKFKPMNPKI
IPCNESFNNDPPCSCVDCISSCPIAQEVKKNSENFKILNYDGYIFIIMLIFFIGSLMFTV
FANRKVPSKEMNHIKNKNFELSMSEQYAQKVEKFLQEIFTNWGKFCATHPLKVIFISLLL
VACFAYGTRFSQVTVDPIELWASSTSQSRIQKDFFDSKFDPFYRVEQVIITAKGYQDIIH
NTSNGVINFGPAFNKEFLLKVLEIQQSIENIDNGVLKDICFAPLRSANLPKDEYEVTDCL
VQSIWGYFQNRKKEITDPKRNNRKDKNNFTVNYLDTLYNCFQNPFDTTCFATYKGPIDPA
VALGGFNENNDTMPKNPKYERASSVILTFLLNNYNDDLKVKAAKEWEEKFVKLMQNYTRN
ENNSMIDIAFISERSIEDELDRGSKSDISTIIMSYLIMFVYIAVALGHVNGLSRLMIDSK
ITLGVGGVVIVLASVAASSGFFGYCGVSATLIIFEVVPFLVLAVGVDNIFILVQTHQRES
REISETNAEHIGRILGKVGPSILLTSLSECTCFFLGALTDMPAVKAFALYAGMALLFDFL
LQISCFVSLLALDTARQNENRWDIFCIIRGPKKSAQIQGNNESVLYKFFKFFYVPLLMKK
PVRIAVIIVFFGWLCSSIAVISKVEVGLDQELSMPKDSFVYKYFQHLKKYLSIGPPVYFI
LKGDLNMSNTQIQNMICGGINCNFDSLSTQIYLASQVPGNTYIARPASSWLDDYFDWSQL
QTCCKQQDSTKEFCPHSEEFDCHTCNIVKNEFNRPVDSNFSYFINFFLQDNPDEDCAKGG
HAAYSKAVEILKNNKIGASYFMSYHTILKTSQDYYEALRSAREISQNITKTMRSKLQEIG
QPDNVEVFPYSVFYVFYEQYLTMYPDTIRSLGISLLAIFIVTFLLMGFDFRLSSVVTLTI
AMIVINIGGLMYFWNISLNAVSLVNLVMAVGISVEFCSHLVHSFRVSTKHTHLERAEDSL
IKMGSSIFSGITLTKFGGIFILGFAQSQIFQVFYFRMYLGIVLYGAAHGLVFLPVLLTFI
GGRRKLNDENIEDPVETPLKDMNEIAIDESK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12952.t1 | Coils | Coil | Coil | 583 | 603 | - |
| 8 | g12952.t1 | Gene3D | G3DSA:1.20.1640.10 | Multidrug efflux transporter AcrB transmembrane domain | 1090 | 1271 | 7.1E-11 |
| 4 | g12952.t1 | PANTHER | PTHR45727 | NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1 | 26 | 1265 | 0.0 |
| 1 | g12952.t1 | Pfam | PF16414 | Niemann-Pick C1 N terminus | 33 | 281 | 3.5E-70 |
| 2 | g12952.t1 | Pfam | PF12349 | Sterol-sensing domain of SREBP cleavage-activation | 656 | 809 | 5.2E-57 |
| 3 | g12952.t1 | Pfam | PF02460 | Patched family | 1066 | 1259 | 1.2E-32 |
| 24 | g12952.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 25 | g12952.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 26 | g12952.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 16 | - |
| 40 | g12952.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 19 | g12952.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 281 | - |
| 36 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 282 | 302 | - |
| 11 | g12952.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 303 | 350 | - |
| 39 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 351 | 368 | - |
| 17 | g12952.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 369 | 627 | - |
| 33 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 628 | 649 | - |
| 10 | g12952.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 650 | 660 | - |
| 34 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 661 | 684 | - |
| 21 | g12952.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 685 | 689 | - |
| 37 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 690 | 713 | - |
| 12 | g12952.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 714 | 733 | - |
| 27 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 734 | 756 | - |
| 22 | g12952.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 757 | 767 | - |
| 32 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 768 | 792 | - |
| 16 | g12952.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 793 | 841 | - |
| 31 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 842 | 861 | - |
| 20 | g12952.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 862 | 1107 | - |
| 29 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1108 | 1128 | - |
| 15 | g12952.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1129 | 1134 | - |
| 35 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1135 | 1154 | - |
| 18 | g12952.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1155 | 1159 | - |
| 30 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1160 | 1182 | - |
| 14 | g12952.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1183 | 1202 | - |
| 38 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1203 | 1225 | - |
| 23 | g12952.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1226 | 1236 | - |
| 28 | g12952.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1237 | 1260 | - |
| 13 | g12952.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1261 | 1291 | - |
| 54 | g12952.t1 | ProSiteProfiles | PS50156 | Sterol-sensing domain (SSD) profile. | 627 | 792 | 39.512 |
| 6 | g12952.t1 | SUPERFAMILY | SSF82866 | Multidrug efflux transporter AcrB transmembrane domain | 615 | 792 | 1.1E-18 |
| 5 | g12952.t1 | SUPERFAMILY | SSF82866 | Multidrug efflux transporter AcrB transmembrane domain | 1067 | 1260 | 2.75E-24 |
| 7 | g12952.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 53 | g12952.t1 | TIGRFAM | TIGR00917 | 2A060601: Niemann-Pick C type protein family | 35 | 1261 | 0.0 |
| 48 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 280 | 302 | - |
| 52 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 351 | 368 | - |
| 46 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 630 | 652 | - |
| 49 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 665 | 687 | - |
| 42 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 691 | 713 | - |
| 50 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 768 | 790 | - |
| 45 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 842 | 864 | - |
| 41 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1111 | 1128 | - |
| 47 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1132 | 1154 | - |
| 43 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1161 | 1183 | - |
| 51 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1203 | 1225 | - |
| 44 | g12952.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1238 | 1260 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005319 | lipid transporter activity | MF |
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K12385 (Niemann-Pick C1 protein)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
