Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein transport protein Sec31A.

Parent gene

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_2 g7533 g7533.t1 TSS g7533.t1 24373727 24373727
chr_2 g7533 g7533.t1 isoform g7533.t1 24373964 24378620
chr_2 g7533 g7533.t1 exon g7533.t1.exon1 24373964 24375386
chr_2 g7533 g7533.t1 cds g7533.t1.CDS1 24373964 24375386
chr_2 g7533 g7533.t1 exon g7533.t1.exon2 24375439 24375539
chr_2 g7533 g7533.t1 cds g7533.t1.CDS2 24375439 24375539
chr_2 g7533 g7533.t1 exon g7533.t1.exon3 24375841 24377301
chr_2 g7533 g7533.t1 cds g7533.t1.CDS3 24375841 24377301
chr_2 g7533 g7533.t1 exon g7533.t1.exon4 24377797 24378237
chr_2 g7533 g7533.t1 cds g7533.t1.CDS4 24377797 24378237
chr_2 g7533 g7533.t1 exon g7533.t1.exon5 24378297 24378368
chr_2 g7533 g7533.t1 cds g7533.t1.CDS5 24378297 24378368
chr_2 g7533 g7533.t1 exon g7533.t1.exon6 24378432 24378620
chr_2 g7533 g7533.t1 cds g7533.t1.CDS6 24378432 24378620
chr_2 g7533 g7533.t1 TTS g7533.t1 24378856 24378856

Sequences

>g7533.t1 Gene=g7533 Length=3687
ATGAAAATTAAAGAACTACAGAAATCTGTTAATGTCGCCTGGTCACCTGAAAAGCAAACG
CCTATTTATTTAGCAGCTGGATCAGCGGCACAGCAATTACTTGACACTTCTTTTAATAGT
ACTAATCCAACATTAGAACTTTATAGTCTTAATCTCTCAGACTCTAGTTATGATTTGGAG
CTCGTTGGTGTTCAACAGAGTAGTCACAAATTTCACAAACTTATTTGGAGTTCATTTGAT
AACTCGAATCAATTTACAAACGGTCTTATTGTTGGTGGTTGCGAGAGCGGCTACTTAAAA
ATATATAATGTTTCAAAGATGTTGGCTGGAGAAGATGCACTCGTTGCACAATCTGATAAG
CATAGTGGACCAGTAAGAACTCTAGACTATAATCCATTTAAAACGAACTTGATAGCATCG
GCGACATCTGAGTCAGAAATTATTGTGTGGGATGTGAATAATCTTGCTATGCCGATGACA
CCGGGACAAAAGTCACAACCTTTAGAAGATGTGTGTGGTGTTGCTTGGAACTTGCAAGTT
CAGCATGTATTAGCTTCAACTTTTGCTACTAGATGTTGCATTTGGGATTTGCGAAAAAAT
GAACAGGTAGTTAAATTGACTGATTCACAATCGCGAGTGAGATGGCGTGTAATTCAATGG
CATCCTGAAATTGCTACACAACTTTGGCTTGCATCAGAAGATGATCAAACTCCAGTAATT
CAACTTTGGGATTTGAGATATGCAACTGCTCCATCAAAAACATTGCAAATTCACTCGAGA
GGTGTGTTAGGTATGCATCTTTCAAGTAAAGACACTGAACTTATGGTCTCATGTGCAAAA
GACAACAAAATACTATGTTGGAATGCAAATTCAGAAGATAATCATGGTGAAATTTTATCA
GAACTTGCATCAACAAGTCAATGGTATTCTGATGTTTCATGGTGTCCAAGAAATCCAGCT
CTTATTGCTGCATCAAGCTTCGATGGCAATGTTTCAATCTATTCAGTTTTTGGTGGAATA
CAACATCAAGTTCAAACTACAAGTAAAATTGCAGATTCATTTCCTGGTATGGAGCAAATA
CCGCAAGAACATTTATCGCAACCACATAATGTTCATGTATATCACGATTTAAAAAAGCCT
CCAAAATGGTTAAGACGTCCAACAGGCATCTCATTTGCATTTGGTGGTAAATTCGCAACA
TTTGATAGCAGCACTAGGACTATTCAAATAAAACAACTTGTGACTGACGAAAAGCTTGTA
AAAAATTCAAGAGATCTCGAAAATGTTTTAACACAAGGCACATTTGCTGATTATTGTCGT
CAAAAAGCTGATGAATGTAACGATCAGAACAAACGATACATTTGGTACTTTTTAAAAGCA
TACTTTGAAGAAAATCCAACAAAAGAATTTTTAAATTTGCTTGGATATCATACAGATGAC
ATGGTATCAAAATTGAGCAAATTCACTGAAACAAAAGATTCGGCTGTTGATGGAGTAACT
AGTAAAATGGCTCAATTGAATCGAAATCAAGATGGTTTTGATATTAATGGCATCAATGAA
TCCAACATTCAATACAAATTGGCAACAAGCGGTTCAGAAGGTTTAATTTGTGAGGCTCTA
CTTACAGGAAATATTGCTGCAGCAGTTGAATTGTGTATGAATGCCGGTCGTTCAACAGAT
GCAATTATACTTGCCTCATTGGGAGGAAGTGATTTGTTAGCAAAAACTCAATACCGCTAT
TTAAAAAATAATGACAGTTTCATTTCGAATCTAATTTCTGCAATGGTAATGGCAGATTGG
AGTGGAGTTATATCACAATGTACAATTGATTCATGGAAAGAGGCATTAGTTGCTGCATTG
ACTCATAGTAAAGAACAATCAGGTCTTTTGTGTGAGCGACTTGGTGAAAGAATGCAAATG
GAATCTGGTGGTGATTTATCAATTATGAAAGATTCTATTTTATGCTACATTTGCTCTGGA
AATGTAGAAAGAATTGTTGATGCATGGAGCACAATAAATGGACCAGATTCATTTGAGGAT
TCAGAAAAGTTGCAAGAATTGATAGAAATGGTTGTTTTACTTAATAAAGGCATGGAAATG
CATGGACAAAATATTCAAGTTTATGGAAAATATGCTGAACTTTTGTCAAAATATGCTTCG
TTGTTAGCAGCACAAGGTTCTTTAGAATTGGCATTAACTTACATTGGGACTTCATGTGAC
GATCAAAATATTGTAGAATTACGTGATCGTCTTTATTATGCTCTTGGTCATAAACAGCAG
CAGCAACACCAATATCAACAAAAACAGAGAGGATCATCTGCTTTTCAGAATCCTTATCAA
AGTGCACCTCGTGCTTCTAGAACATTATCAGTTTCATCAACAGGCATGCCACCAGCAACA
ACTTTCAATACTGGTTTACCTAATTCTGCTTTAAATAATAGTTTTGTTGATCAGAATCAA
ATGTGGCAGCCACAACAACCACAAGTTTCTAATGCACCACCGCCAATGATTCCTCTTCAA
TCAGTTCCTAAAATGACTTCATCAGTTATGAATCCAATGGAAAGTATGCCACAGCCGCCA
CGTCCATCAAGCGTATCAAGTGTTTCTAGTCAACCGACTACAACTTCTTCTGCACCTAAG
CCTAAACGTTTATTAGATCCATCAGTTTCATCGAATCCTGGATATGGACAAATGCCAACT
GTTGCACCATATAATCCAAATACATTCAATACAAATGCCGTTCAACCAACATTTAATACA
CAAGCTATTAATAATCCAACGATGCCGATTCAACAGCAACCACCTGCAACGATGATGGGC
TATGATCATTTTAATCAAAATCCAATGTCTTATGGCTATCAAAATAATACTATGCAGATG
AATGGATCTTTTGCTCCTCCTCCATCAATGCCACAAAATGTTCAAAAAAATCCAACACCT
CCTCCAGGATGGAACGATCCTCCAGAATTCAAATCAAAACCTCAGCCCAAAAAAGAGATA
GCAGCCGTTGCTCCCATTATGCATCCAATTTTCGGAAGTGCAGATGTGACACCGGTTCCA
CAAGTGCCTACTGCAAATAACAATGTCATGACTCCTGGTATGCCTCTTCAAAATCAATAT
AATCAAAATTACATGATACCACAGGCTACAGTTAATCCAATGAATATGAATACTGGAAGT
TTTTATCCATCGCCGCAGCAGCAACAGCCAGTTCAAGAAGTGCAAGATCCTAATAACTTG
ATCAATTATTCAAATTTTAATAATTTTGCTAGTGTTCAAACACAAATGCAACCGCAACAA
TCCCAATCGCCACAACCAAGCGTTCCAGCTGTTCGTGAAAAACCTCCGCTTCCTGAAGAA
TATATTTATTTGCAAACTGTATTAGACGAACTTAAGACGCAATGTATTAACAGAGCAACA
AATCCTCAAATGAAAAGAAAACTTGATGACGTCTCAAAGCGATTGGAATCACTTTATGAT
TTATTGCGTGAGAATAGGTTATCTACGAATACACTCGATTCGTTAAATCAAATGGTGCAA
TTGATAACTATAGGCGATTATGCTCATTGTTTAGGACTTCATACACAAATGGTTTCAGGT
CCTGAATTTGCCAAGATAGCAAGTTTTATGCCTGGAATAAAAATTCTGCTTCAATTGGCT
ATTCAGTTGCAAGTCTTTTTACGATAA

>g7533.t1 Gene=g7533 Length=1228
MKIKELQKSVNVAWSPEKQTPIYLAAGSAAQQLLDTSFNSTNPTLELYSLNLSDSSYDLE
LVGVQQSSHKFHKLIWSSFDNSNQFTNGLIVGGCESGYLKIYNVSKMLAGEDALVAQSDK
HSGPVRTLDYNPFKTNLIASATSESEIIVWDVNNLAMPMTPGQKSQPLEDVCGVAWNLQV
QHVLASTFATRCCIWDLRKNEQVVKLTDSQSRVRWRVIQWHPEIATQLWLASEDDQTPVI
QLWDLRYATAPSKTLQIHSRGVLGMHLSSKDTELMVSCAKDNKILCWNANSEDNHGEILS
ELASTSQWYSDVSWCPRNPALIAASSFDGNVSIYSVFGGIQHQVQTTSKIADSFPGMEQI
PQEHLSQPHNVHVYHDLKKPPKWLRRPTGISFAFGGKFATFDSSTRTIQIKQLVTDEKLV
KNSRDLENVLTQGTFADYCRQKADECNDQNKRYIWYFLKAYFEENPTKEFLNLLGYHTDD
MVSKLSKFTETKDSAVDGVTSKMAQLNRNQDGFDINGINESNIQYKLATSGSEGLICEAL
LTGNIAAAVELCMNAGRSTDAIILASLGGSDLLAKTQYRYLKNNDSFISNLISAMVMADW
SGVISQCTIDSWKEALVAALTHSKEQSGLLCERLGERMQMESGGDLSIMKDSILCYICSG
NVERIVDAWSTINGPDSFEDSEKLQELIEMVVLLNKGMEMHGQNIQVYGKYAELLSKYAS
LLAAQGSLELALTYIGTSCDDQNIVELRDRLYYALGHKQQQQHQYQQKQRGSSAFQNPYQ
SAPRASRTLSVSSTGMPPATTFNTGLPNSALNNSFVDQNQMWQPQQPQVSNAPPPMIPLQ
SVPKMTSSVMNPMESMPQPPRPSSVSSVSSQPTTTSSAPKPKRLLDPSVSSNPGYGQMPT
VAPYNPNTFNTNAVQPTFNTQAINNPTMPIQQQPPATMMGYDHFNQNPMSYGYQNNTMQM
NGSFAPPPSMPQNVQKNPTPPPGWNDPPEFKSKPQPKKEIAAVAPIMHPIFGSADVTPVP
QVPTANNNVMTPGMPLQNQYNQNYMIPQATVNPMNMNTGSFYPSPQQQQPVQEVQDPNNL
INYSNFNNFASVQTQMQPQQSQSPQPSVPAVREKPPLPEEYIYLQTVLDELKTQCINRAT
NPQMKRKLDDVSKRLESLYDLLRENRLSTNTLDSLNQMVQLITIGDYAHCLGLHTQMVSG
PEFAKIASFMPGIKILLQLAIQLQVFLR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g7533.t1 Gene3D G3DSA:2.130.10.10 - 1 337 1.1E-91
15 g7533.t1 Gene3D G3DSA:1.25.40.1030 - 373 756 1.0E-99
16 g7533.t1 Gene3D G3DSA:1.20.940.10 Functional domain of the splicing factor Prp18 1119 1225 3.2E-7
13 g7533.t1 MobiDBLite mobidb-lite consensus disorder prediction 762 793 -
11 g7533.t1 MobiDBLite mobidb-lite consensus disorder prediction 850 886 -
12 g7533.t1 MobiDBLite mobidb-lite consensus disorder prediction 850 881 -
9 g7533.t1 MobiDBLite mobidb-lite consensus disorder prediction 1093 1108 -
10 g7533.t1 MobiDBLite mobidb-lite consensus disorder prediction 1093 1113 -
2 g7533.t1 PANTHER PTHR13923 SEC31-RELATED PROTEIN 1 1004 1.3E-296
1 g7533.t1 PANTHER PTHR13923 SEC31-RELATED PROTEIN 910 1221 1.3E-296
17 g7533.t1 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 118 344 12.895
18 g7533.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 118 160 10.308
8 g7533.t1 SMART SM00320 WD40_4 58 103 150.0
4 g7533.t1 SMART SM00320 WD40_4 111 151 0.0054
5 g7533.t1 SMART SM00320 WD40_4 161 196 39.0
7 g7533.t1 SMART SM00320 WD40_4 248 288 0.016
6 g7533.t1 SMART SM00320 WD40_4 295 335 0.091
3 g7533.t1 SUPERFAMILY SSF50978 WD40 repeat-like 12 336 6.41E-37

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:0005515 protein binding MF
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport BP

KEGG

Orthology

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.

Raw TPM values