General information for g12952.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as NPC intracellular cholesterol transporter 1 homolog 1b.
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.t4 | isoform | g12952.t4 | 27110942 | 27114877 |
| chr_1 | g12952 | g12952.t4 | exon | g12952.t4.exon1 | 27110942 | 27111383 |
| chr_1 | g12952 | g12952.t4 | cds | g12952.t4.CDS1 | 27110944 | 27111383 |
| chr_1 | g12952 | g12952.t4 | exon | g12952.t4.exon2 | 27111446 | 27111770 |
| chr_1 | g12952 | g12952.t4 | cds | g12952.t4.CDS2 | 27111446 | 27111770 |
| chr_1 | g12952 | g12952.t4 | exon | g12952.t4.exon3 | 27112240 | 27112541 |
| chr_1 | g12952 | g12952.t4 | cds | g12952.t4.CDS3 | 27112240 | 27112541 |
| chr_1 | g12952 | g12952.t4 | exon | g12952.t4.exon4 | 27112597 | 27112756 |
| chr_1 | g12952 | g12952.t4 | cds | g12952.t4.CDS4 | 27112597 | 27112756 |
| chr_1 | g12952 | g12952.t4 | exon | g12952.t4.exon5 | 27112854 | 27113087 |
| chr_1 | g12952 | g12952.t4 | cds | g12952.t4.CDS5 | 27112854 | 27113087 |
| chr_1 | g12952 | g12952.t4 | exon | g12952.t4.exon6 | 27114830 | 27114877 |
| chr_1 | g12952 | g12952.t4 | cds | g12952.t4.CDS6 | 27114830 | 27114877 |
| chr_1 | g12952 | g12952.t4 | TSS | g12952.t4 | 27115022 | 27115022 |
| chr_1 | g12952 | g12952.t4 | TTS | g12952.t4 | NA | NA |
Sequences
>g12952.t4 Gene=g12952 Length=1511
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
AATAATAGAAA
>g12952.t4 Gene=g12952 Length=503
MCKLQLRLLKLLLLIVTTLLGQRLVKCDVKQSNSCVWYGICDRVKEYNSVKIKNCAYDGP
PKKLDSNGVFALNEWCSHLREDDDDVYTCCDNEQLYALNENIKQASNLLNRCPACMKNFA
KHICDYICSPRHGEFINVLKKKQSISKPNKEYIDEIDLFVTEDYLNGTYDSCKNVLMPST
GQKVMDMMCGGFPASKCSPMRWFQHMGDVNVAQIPFQINYIPQKSLMTSDNKFKPMNPKI
IPCNESFNNDPPCSCVDCISSCPIAQEVKKNSENFKILNYDGYIFIIMLIFFIGSLMFTV
FANRKVPSKEMNHIKNKNFELSMSEQYAQKVEKFLQEIFTNWGKFCATHPLKVIFISLLL
VACFAYGTRFSQVTVDPIELWASSTSQSRIQKDFFDSKFDPFYRVEQVIITAKGYQDIIH
NTSNGVINFGPAFNKEFLLKVLEIQQSIENIDNGVLKDICFAPLRSANLPKDEYEVTDCL
VQSIWGYFQNRKKEITDPKRNNR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12952.t4 | PANTHER | PTHR45727 | NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1 | 26 | 498 | 9.9E-113 |
| 1 | g12952.t4 | Pfam | PF16414 | Niemann-Pick C1 N terminus | 33 | 281 | 5.3E-71 |
| 8 | g12952.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 9 | g12952.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 10 | g12952.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 16 | - |
| 13 | g12952.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 7 | g12952.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 281 | - |
| 11 | g12952.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 282 | 302 | - |
| 5 | g12952.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 303 | 350 | - |
| 12 | g12952.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 351 | 368 | - |
| 6 | g12952.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 369 | 503 | - |
| 4 | g12952.t4 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 3 | g12952.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 280 | 302 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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. There were no conditions that were differentially expressed