General information for g14469.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein patched.
Parent gene
- The parent gene g14469 is located on chr_4: 732748..745705 (+ 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_4 | g14469 | g14469.t1 | isoform | g14469.t1 | 732748 | 745705 |
| chr_4 | g14469 | g14469.t1 | exon | g14469.t1.exon1 | 732748 | 732891 |
| chr_4 | g14469 | g14469.t1 | cds | g14469.t1.CDS1 | 732748 | 732891 |
| chr_4 | g14469 | g14469.t1 | exon | g14469.t1.exon2 | 740950 | 741503 |
| chr_4 | g14469 | g14469.t1 | cds | g14469.t1.CDS2 | 740950 | 741503 |
| chr_4 | g14469 | g14469.t1 | exon | g14469.t1.exon3 | 742354 | 742870 |
| chr_4 | g14469 | g14469.t1 | cds | g14469.t1.CDS3 | 742354 | 742870 |
| chr_4 | g14469 | g14469.t1 | exon | g14469.t1.exon4 | 742968 | 744100 |
| chr_4 | g14469 | g14469.t1 | cds | g14469.t1.CDS4 | 742968 | 744100 |
| chr_4 | g14469 | g14469.t1 | exon | g14469.t1.exon5 | 744164 | 744839 |
| chr_4 | g14469 | g14469.t1 | cds | g14469.t1.CDS5 | 744164 | 744839 |
| chr_4 | g14469 | g14469.t1 | exon | g14469.t1.exon6 | 744932 | 745705 |
| chr_4 | g14469 | g14469.t1 | cds | g14469.t1.CDS6 | 744932 | 745705 |
| chr_4 | g14469 | g14469.t1 | TSS | g14469.t1 | NA | NA |
| chr_4 | g14469 | g14469.t1 | TTS | g14469.t1 | NA | NA |
Sequences
>g14469.t1 Gene=g14469 Length=3798
ATGGGTTTACCAATAAACGATTCAATACCACGAGTGCCAGAGCCTCATTCAGAATTAACA
ATTGAAGATGAAAAACTTTATTCTGACCTGTATATTAGAACAAGCTGGTTTGATGCGGCC
TTGGCTTTAGATCAAATTGAGAAGGGCAAAGCAGATGGACGAAGAACGAGCATTTACCTG
CGCCATCTATTTCAATCACATTTTTTTAAAATTGGTCGAAGTATTGACAAGCATGCAGGA
ATTATTATTTTCATGGCTGCTCTTATTCTCGGCACATTTTGTGTTGGTCTTAAATCCGTC
ATAATTCACTCAAATGTAAATCAATTGTGGCTGGAAGTGGGTGGAAGTCTTGAACAAGAA
CTTGCCTATACTGACAAATACCTTGGTTACATTGATACATCAACAAACAATCAATTGCTA
ATACAAACGCTTAAAAATGAAGATGCAACGATACTTTATGACCAAGCTTTACTTTCGCAT
CTGAAAGTAGTCAAACAAGCACTTGGAGTTGAAGTTTTTATTGGTGAAGTTACGTGGACA
TTAAAAGATCTTTGTCAATTGCCATCAAGTCCACGATTTGATGAGCATTTTATGGAGCAA
ATTTTGGAAATTGTGATACCATGCGCAATTATTACACCGCTTGATTGTTTTTGGGAGGGC
AGCAAATTACTTGGACCTGACAGAGATCCTCATATACCAATGATAAATGAAAAGTATGGA
ACAATAAGTTGGCAATCATTAGATCCAGCAAGATTACTTGAAGATGCCAGTAAATCTTTT
CATACTGAAGACAAATCATCGAAATCTGATCAAGGAATGATTGCAAAAGTTGAACAATAT
ATGAAACAAGCTGGAATAACAACTGGTTACATCAAAAAACCTTGTCTTAATCCATTTGAT
CCACAATGTCCAGCATCATCACCAAATAAAAGATCAAGACAAACTCCCGACATTGGTGCA
GCTTTGAGTGGTGGTTGTTATGGTTATGCAATGAATTTCATGCATTGGCCTGAAGAATTG
ATTGTTGGTGGTGCTGAAAAGAATGCAACTAATCACATTAAGAAAGCTAAGGCATTACAG
ACAGTCATTCAATTGATGAGCGAGCAAGAACTTTATGATCATTGGCATGATAACTATAAA
ACCCATTATGCTGGATGGAGTTTAAAGAAAGCTAAAGAAGTACTGAATGCATGGCAGGAA
AAATTTTCTAATGAAGTTCGTAAAATAATGCGTGAAGAAGGAAATACAACATATTCAGCA
TATGATTTCAATGCATTTAGTTCAACAACTTTAAACAATTCACTTCGAGCTCATTCAAAG
CCAGATTTTTTGCATTTATCGATTTGTGTCATTATTATAATGGTCTATACTGGATTAGTT
CTTTATCGTTTTGGTGATCCTGTTAATGGTCAATCAGGTGTTGGAATGTTTGGAATTCTT
TTATTATGTGCATCAACTGCTGCTGGTCTTGGTGTTTGTTCACTGCTTGGATTAGCTTTT
AATGTCTCAACAACTCAAGTTGTGCCATTAATTGCACTTGGACTTGCTGTTGATCAAATT
TTCATTCTTACTCATGGCTATGACAGTCGTAGAAATAGCAATGAACAAATGCATACAGCA
CAAATAATGAAAAAGTATGGATTGAGTGTACTCTTTAATGGTGCATCAACTGCAAGTGCA
TTTTTAGGTGCTGCTTTACTGCCAATTCCAATTTTAAGAACTTTTGCATTGCAAGCAACA
ATTTTGATAACTGTCAATCTTTTTGCTATTTTATTTGTCTTTCCTGCATTCATCACACTC
GATTTAAGACGAAGACGATCGTCACATATGGATATTTTCTGCTGCTTACCAACATTCACA
AAAGTTCATCATCCTATTGAAACTGTCAACAATGATTCATTACTAAATAAACCTAAAAAG
TGTCAAAAATTAACTATTAAACTTTATATTGATTTAATTTTAAATGGAAAAATGAAAGCA
CTTGGTATTTTTACAATTTTGGTAATTTTTGTCTGTTCAACTTATGCAACAATAAAACTT
CAAGATGGTTTTGAACTTACTGACTTAATACCTAAAAACACAAGTGAACACAATTTCATA
TCAGCACAAAGCAATCTTTTTGGTTTCTACAACATTTATGCAGTGACGCAAGGCAATTTT
GAATATCCACAAAATCAGAAATTACTTAGGGAATATCATGAGGCATTCATTAGAGTTCCT
TATATAATAAAAAATGACAATGGTGGCTTACCTGACTTTTGGTTAAATCAATTTAGAGAT
TGGTTGAAAAATTTACAAAATGCTTTTGATAGAGATTATAAAAGTGGTGCTATCAGCAAA
GAAAGATGGTACGCAAATGCATCAGCTGATGGAATTTTAGCCTTCAAATTGCTTGCTCAA
ACTGGACATGTTGACAATCCAATTGACAAATCACTCATCACTCACAATCGACTCGTAAAT
TCTGATGGAATAATCAATCCAAAAGCTTTTTATAATTATCTCTCAGCATGGGCATGGAAT
GATGCTGCTTATGGTGCATCACAGAGCAATCTTCGACCATCACCAAGAATGTGGATTCAT
TCACCAAAAGACAAGCATATGGAAATCCCTAAAAGTGCACCACTTTCATATACACAATTG
CCATTTTATCTTCATGGTCTTTACACAACAAAAGACATTAAAAATGTGATTGAAGAAATT
CGAGAACTTTGCACAAAATTCAATGCTCGTGGTCTACCAAATTATCCATCTGGCATTCCA
TTCCTTTATTGGGCTCAGTATTTTAATCTTCATGTACTTATTGGACTTGCACTTGCTGGA
TCAATTTTGGTTACTTTTGTGCTAAGCATTATTTTCCTACAATCAGTGTCGGCATCAATT
TTGGTTATTTTAAATGCGATTTTTGTCTTTGCTCAATTATTTGGAGTTATGTTGGTTCTG
GATGTAAAATTATCAGCAATTGCTGCTGTTATTTTGATTGCTAGTATTGGATTGAGCATT
TGCTTTACTGCTAATATTACTTTGGGCTTTCTAACATCAATTGGCAATCGAGAACGTCGA
CTTCGTCTAGCACTTGAGCATACAATTCCATACATTTTGCACAGTATCACAACTTCAATT
CTTATCCTACTCATTCTCTATTTCTCACCATTTGAATTCATCGTCAAACACTTTTTCTAT
CTTCTCATTTCATTCTGGCTTGTTTGTGCAGTCAATTCGCTCTTTCATTTTCCAATGTTG
TTATTACTTTTTGGTATGCGACCAGAACTTGTACCATATCAACATCAAAATCGAATTTCA
ACACCGTCACCACAATTGAAATCAATCAATAGCTCAAAATCATCAGGCAAAGCAATCACA
TTGCATAATAAACGAACATGCAGGAAGAAATCACATCATTGTCATGTGAAGAATACAAAT
CTTAATAATGAGCAATCATTAACAACTATAACAGAAGAACCATCTTGGCAATCATCAGCA
TCATCATTGTCAAATGCTTCAGGCTACATAAGTGATGGAAATAAATCAAATAGAAATTTC
ACAAGAGTTCATAACAATACAAAACAAGACAATAGTAATACAGCAAATGTAAATTCAATA
AATATCGATGCAGCAACTGCAGCAGCACAGCAAGCATTTAAAAGTATAATAGTGCAGCCA
GAAGTAACTGTTGAAACACATCATAATGGCAATCAACAAAATACAAAAGTTACTGCAACT
GCAAATATTAAACTTGAATTTACAACTGGAGGCAGTGGGAGTGGAAGTGACAGTGATGTG
AAGAAGGAAAATTGTTGA
>g14469.t1 Gene=g14469 Length=1265
MGLPINDSIPRVPEPHSELTIEDEKLYSDLYIRTSWFDAALALDQIEKGKADGRRTSIYL
RHLFQSHFFKIGRSIDKHAGIIIFMAALILGTFCVGLKSVIIHSNVNQLWLEVGGSLEQE
LAYTDKYLGYIDTSTNNQLLIQTLKNEDATILYDQALLSHLKVVKQALGVEVFIGEVTWT
LKDLCQLPSSPRFDEHFMEQILEIVIPCAIITPLDCFWEGSKLLGPDRDPHIPMINEKYG
TISWQSLDPARLLEDASKSFHTEDKSSKSDQGMIAKVEQYMKQAGITTGYIKKPCLNPFD
PQCPASSPNKRSRQTPDIGAALSGGCYGYAMNFMHWPEELIVGGAEKNATNHIKKAKALQ
TVIQLMSEQELYDHWHDNYKTHYAGWSLKKAKEVLNAWQEKFSNEVRKIMREEGNTTYSA
YDFNAFSSTTLNNSLRAHSKPDFLHLSICVIIIMVYTGLVLYRFGDPVNGQSGVGMFGIL
LLCASTAAGLGVCSLLGLAFNVSTTQVVPLIALGLAVDQIFILTHGYDSRRNSNEQMHTA
QIMKKYGLSVLFNGASTASAFLGAALLPIPILRTFALQATILITVNLFAILFVFPAFITL
DLRRRRSSHMDIFCCLPTFTKVHHPIETVNNDSLLNKPKKCQKLTIKLYIDLILNGKMKA
LGIFTILVIFVCSTYATIKLQDGFELTDLIPKNTSEHNFISAQSNLFGFYNIYAVTQGNF
EYPQNQKLLREYHEAFIRVPYIIKNDNGGLPDFWLNQFRDWLKNLQNAFDRDYKSGAISK
ERWYANASADGILAFKLLAQTGHVDNPIDKSLITHNRLVNSDGIINPKAFYNYLSAWAWN
DAAYGASQSNLRPSPRMWIHSPKDKHMEIPKSAPLSYTQLPFYLHGLYTTKDIKNVIEEI
RELCTKFNARGLPNYPSGIPFLYWAQYFNLHVLIGLALAGSILVTFVLSIIFLQSVSASI
LVILNAIFVFAQLFGVMLVLDVKLSAIAAVILIASIGLSICFTANITLGFLTSIGNRERR
LRLALEHTIPYILHSITTSILILLILYFSPFEFIVKHFFYLLISFWLVCAVNSLFHFPML
LLLFGMRPELVPYQHQNRISTPSPQLKSINSSKSSGKAITLHNKRTCRKKSHHCHVKNTN
LNNEQSLTTITEEPSWQSSASSLSNASGYISDGNKSNRNFTRVHNNTKQDNSNTANVNSI
NIDAATAAAQQAFKSIIVQPEVTVETHHNGNQQNTKVTATANIKLEFTTGGSGSGSDSDV
KKENC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g14469.t1 | PANTHER | PTHR46022:SF1 | PROTEIN PATCHED | 36 | 1113 | 0.0 |
| 4 | g14469.t1 | PANTHER | PTHR46022 | PROTEIN PATCHED | 36 | 1113 | 0.0 |
| 1 | g14469.t1 | Pfam | PF12349 | Sterol-sensing domain of SREBP cleavage-activation | 469 | 616 | 7.7E-26 |
| 2 | g14469.t1 | Pfam | PF02460 | Patched family | 884 | 1084 | 1.9E-8 |
| 24 | g14469.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 78 | - |
| 38 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 79 | 101 | - |
| 29 | g14469.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 102 | 442 | - |
| 33 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 443 | 462 | - |
| 26 | g14469.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 463 | 473 | - |
| 43 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 474 | 500 | - |
| 32 | g14469.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 501 | 505 | - |
| 40 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 506 | 527 | - |
| 22 | g14469.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 528 | 547 | - |
| 39 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 548 | 569 | - |
| 31 | g14469.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 570 | 574 | - |
| 35 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 575 | 600 | - |
| 25 | g14469.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 601 | 659 | - |
| 36 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 660 | 678 | - |
| 28 | g14469.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 679 | 929 | - |
| 44 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 930 | 953 | - |
| 23 | g14469.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 954 | 959 | - |
| 42 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 960 | 980 | - |
| 30 | g14469.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 981 | 985 | - |
| 41 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 986 | 1011 | - |
| 21 | g14469.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1012 | 1030 | - |
| 34 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1031 | 1051 | - |
| 27 | g14469.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1052 | 1056 | - |
| 37 | g14469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1057 | 1084 | - |
| 20 | g14469.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1085 | 1265 | - |
| 19 | g14469.t1 | ProSiteProfiles | PS50156 | Sterol-sensing domain (SSD) profile. | 442 | 600 | 28.4 |
| 18 | g14469.t1 | SUPERFAMILY | SSF82866 | Multidrug efflux transporter AcrB transmembrane domain | 399 | 602 | 1.83E-15 |
| 17 | g14469.t1 | SUPERFAMILY | SSF82866 | Multidrug efflux transporter AcrB transmembrane domain | 914 | 1087 | 1.7E-13 |
| 7 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 102 | - |
| 6 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 443 | 465 | - |
| 14 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 478 | 500 | - |
| 10 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 505 | 527 | - |
| 12 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 548 | 570 | - |
| 13 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 575 | 597 | - |
| 8 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 660 | 678 | - |
| 15 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 931 | 953 | - |
| 5 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 960 | 982 | - |
| 9 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 986 | 1008 | - |
| 11 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1029 | 1048 | - |
| 16 | g14469.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1063 | 1085 | - |
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:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K06225 (patched 1)
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.
