Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein transport protein Sec23A.

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_3 g191 g191.t30 TTS g191.t30 1634353 1634353
chr_3 g191 g191.t30 isoform g191.t30 1634566 1637197
chr_3 g191 g191.t30 exon g191.t30.exon1 1634566 1636608
chr_3 g191 g191.t30 cds g191.t30.CDS1 1634566 1636473
chr_3 g191 g191.t30 exon g191.t30.exon2 1636689 1636970
chr_3 g191 g191.t30 exon g191.t30.exon3 1637098 1637197
chr_3 g191 g191.t30 TSS g191.t30 1637210 1637210

Sequences

>g191.t30 Gene=g191 Length=2425
ATGTACTTTCTCTCCACAAGTTCCAAGTGTAAATTTTCATTTGGTTCAGTGTTAATTAAA
GGAAAATTAAATAAATTAAATATATAACAAGCAAGATTTTTAAAATTAATTGACAACATT
ATGGCAACATACGAAGAATATATTCAACAGAATGAAGATCGTGATGGAATTCGCTTTACG
TGGAACGTTTGGCCCTCGAGCCGTGTTGATGCAACTAAATTAGTTGTGCCTCTTGCTTGC
TTGTATCAACCATTTAAAGAACGAAATGATTTGCCACCAATTATGTATGAGCCTGTCTTG
TGTACGAGAACTACATGTCGTGCTATTTTAAATCCTATGTGTCAAGTTGATTATCGTGCA
AAATTGTGGGTCTGTAACTTTTTTTCCACCACAATATGCTGCAATTTCTGAGCAGCATCA
ACCAGCTGAATTAATACCTGGTTTTAGTACAATTGAGTACACTATTACTCGTGCACCATG
TATGCCTCCAGTTTTTCTGTTCGTAGTCGATACTTGTATGGATGATGAAGAACTAACAGC
CTTGAAAGATTCACTTTCAATGTCATTAAGTTTATTGCCTTCAAATGCACTTGTTGGATT
AATTACTTTTGGTAAAATGGTTCAAGTTCATGAGCTTTGCAATGAAGGATGCTCGAAAAG
TTATGTTTTTCGTGGCACAAAAGATTTGAATGCTAAGCAAATTCAAGATATGCTTGGAAT
TGGAAGAGGTGGTGCTACTATACAACAACAACAGCAGCAACCTCAACAAAGGATGCCACA
ACAGGCACCTCAACCACCAGCAAACAGGTTTTTGCAGCCGTTACAAAAGTGTGACATGGC
ATTGACTGATATGTTGGGTGAAATGCAACGCGATCCTTGGCCTGTATCTCAAGGCAAACG
TCCATTGAGAGCAACTGGTGCGGCTCTTTCAATTGCAGTTGGTTTATTGGAGTGTACTTA
TCCAAATACAGCTGCACGCATTTTACTTTTTGTTGGTGGTCCTTGTTCAACAGGTCCTGG
ACAAGTCGTTGATGATGAATTAAAACATCCAATTCGTTCTCATCATGATATTCATAAAGA
TAATGCAAAATATATGAAAAAAAGTATCAAGCATTATGAAGCACTTGCTTTGCGAACTGC
AACAAATGGGCATTGTATTGACATTTATTCATGTGCACTTGATCAAACTGGTTTGATGGA
AATGAAGCAATGTTGTAATTCAACTGGTGGTCACATGGTAATGGGAGATTCATTCAATTC
TTCACTATTTAAACAAACATTCCAACGTGTCTTTGCCACTGATCCGAAAAATGATCTTAA
AATGGGCTTCAATGCAACTTTAGAAGTGAAATGTTCACGTGAACTTAAAATTGAAGGTGG
CATTGGTCCTTGTGTATCTTTGAATGTTAAAAATGCATCAGTTTCTGAAAATGAAGTTGG
AATGGGTAATACTACTCAATGGAAATTATGCACAATATCACCCAATTCAACAATGGCGTT
GTTCTTTGAAGTTGCTAATCAGCATTCTGCTCCTATACCTCAGGGTGGACGAGGTTGCAT
TCAATTCATAACTCAATATCAACATTCGAGTGGACAAAGAAGAATTCGTGTCACAACTGT
CGCTAGAAATTGGGCAGATGCAACTGTTAACTTGAACTTTATTTCGGCTGGTTTTGATCA
AGAAGCGGCTGCAGTAATTATGGCGAGAATGGTCGTTTATCGTGCTGAATCAGATGATGG
TCCCGATGTTTTACGTTGGATTGATCGTCAGTTGATTCGTTTATGTCAAAAGTTTGGCGA
ATACAACAAGGACGATCCAAATTCATTTAGATTGGCTGAGAACTTTAGCTTATTTCCACA
ATTCATTTATCATTTGAGACGTTCGCAGTTCTTGCAAGTTTTTAATAATTCACCAGATGA
AACAACATTCTATCGTCATATGTTAATGCGAGAAGATTTGACTCAATCATTGATTATGAT
TCAACCAATTTTGTACAGCTACAGTTTCAATGGACCGCCTGAGCCTGTTTTACTTGATAC
ATCCAGTATTCAGCCTGATAAAATCTTATTAATGGACACATTCTTCCAGATATTAATTTT
CCATGGTGAAACAATAGCTCAATGGCGTGCGATGAAATATCACGAAATGAAAGAATATGA
AAATTTCAAACAATTGTTGCAAGCTCCAGTTGATGATGCACAAGAGATTTTGTCAACTCG
ATTCCCTATGCCGCGCTATATTGACACAGAACAAGGCGGTTCACAAGCTCGATTCTTACT
CTCAAAAGTAAATCCATCGCAAACACACAACACGATGTATGGATATGGTGGCCAAGATGG
TGGTGCACCTGTTTTGACAGACGATGTCTCGCTTCAAGTTTTCATGGAGCATTTGAAAAA
ACTAGCTGTCTCATCCACAGCATAG

>g191.t30 Gene=g191 Length=635
MDDEELTALKDSLSMSLSLLPSNALVGLITFGKMVQVHELCNEGCSKSYVFRGTKDLNAK
QIQDMLGIGRGGATIQQQQQQPQQRMPQQAPQPPANRFLQPLQKCDMALTDMLGEMQRDP
WPVSQGKRPLRATGAALSIAVGLLECTYPNTAARILLFVGGPCSTGPGQVVDDELKHPIR
SHHDIHKDNAKYMKKSIKHYEALALRTATNGHCIDIYSCALDQTGLMEMKQCCNSTGGHM
VMGDSFNSSLFKQTFQRVFATDPKNDLKMGFNATLEVKCSRELKIEGGIGPCVSLNVKNA
SVSENEVGMGNTTQWKLCTISPNSTMALFFEVANQHSAPIPQGGRGCIQFITQYQHSSGQ
RRIRVTTVARNWADATVNLNFISAGFDQEAAAVIMARMVVYRAESDDGPDVLRWIDRQLI
RLCQKFGEYNKDDPNSFRLAENFSLFPQFIYHLRRSQFLQVFNNSPDETTFYRHMLMRED
LTQSLIMIQPILYSYSFNGPPEPVLLDTSSIQPDKILLMDTFFQILIFHGETIAQWRAMK
YHEMKEYENFKQLLQAPVDDAQEILSTRFPMPRYIDTEQGGSQARFLLSKVNPSQTHNTM
YGYGGQDGGAPVLTDDVSLQVFMEHLKKLAVSSTA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g191.t30 CDD cd11287 Sec23_C 479 599 6.20739E-84
12 g191.t30 Gene3D G3DSA:3.40.50.410 - 1 268 1.8E-115
14 g191.t30 Gene3D G3DSA:1.20.120.730 - 382 630 1.1E-121
13 g191.t30 Gene3D G3DSA:3.40.20.10 Severin 489 593 1.1E-121
11 g191.t30 MobiDBLite mobidb-lite consensus disorder prediction 72 93 -
5 g191.t30 PANTHER PTHR11141 PROTEIN TRANSPORT PROTEIN SEC23 1 634 0.0
6 g191.t30 PANTHER PTHR11141:SF7 PROTEIN TRANSPORT PROTEIN SEC23A 1 634 0.0
1 g191.t30 Pfam PF04811 Sec23/Sec24 trunk domain 3 259 3.1E-73
3 g191.t30 Pfam PF08033 Sec23/Sec24 beta-sandwich domain 270 373 1.0E-34
2 g191.t30 Pfam PF04815 Sec23/Sec24 helical domain 387 485 1.3E-28
4 g191.t30 Pfam PF00626 Gelsolin repeat 501 587 1.0E-14
10 g191.t30 SUPERFAMILY SSF53300 vWA-like 1 259 6.04E-82
7 g191.t30 SUPERFAMILY SSF81995 beta-sandwich domain of Sec23/24 278 386 8.63E-40
9 g191.t30 SUPERFAMILY SSF81811 Helical domain of Sec23/24 387 489 3.53E-48
8 g191.t30 SUPERFAMILY SSF82754 C-terminal, gelsolin-like domain of Sec23/24 490 631 1.65E-56

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:0006886 intracellular protein transport BP
GO:0030127 COPII vesicle coat CC
GO:0090114 COPII-coated vesicle budding BP
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