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.t28 TTS g191.t28 1634353 1634353
chr_3 g191 g191.t28 isoform g191.t28 1634441 1636601
chr_3 g191 g191.t28 exon g191.t28.exon1 1634441 1636601
chr_3 g191 g191.t28 cds g191.t28.CDS1 1634566 1636509
chr_3 g191 g191.t28 TSS g191.t28 1637210 1637210

Sequences

>g191.t28 Gene=g191 Length=2161
CACAATATGCTGCAATTTCTGAGCAGCATCAACCAGCTGAATTAATACCTGGTTTTAGTA
CAATTGAGTACACTATTACTCGTGCACCATGTATGCCTCCAGTTTTTCTGTTCGTAGTCG
ATACTTGTATGGATGATGAAGAACTAACAGCCTTGAAAGATTCACTTTCAATGTCATTAA
GTTTATTGCCTTCAAATGCACTTGTTGGATTAATTACTTTTGGTAAAATGGTTCAAGTTC
ATGAGCTTTGCAATGAAGGATGCTCGAAAAGTTATGTTTTTCGTGGCACAAAAGATTTGA
ATGCTAAGCAAATTCAAGATATGCTTGGAATTGGAAGAGGTGGTGCTACTATACAACAAC
AACAGCAGCAACCTCAACAAAGGATGCCACAACAGGCACCTCAACCACCAGCAAACAGGT
TTTTGCAGCCGTTACAAAAGTGTGACATGGCATTGACTGATATGTTGGGTGAAATGCAAC
GCGATCCTTGGCCTGTATCTCAAGGCAAACGTCCATTGAGAGCAACTGGTGCGGCTCTTT
CAATTGCAGTTGGTTTATTGGAGTGTACTTATCCAAATACAGCTGCACGCATTTTACTTT
TTGTTGGTGGTCCTTGTTCAACAGGTCCTGGACAAGTCGTTGATGATGAATTAAAACATC
CAATTCGTTCTCATCATGATATTCATAAAGATAATGCAAAATATATGAAAAAAAGTATCA
AGCATTATGAAGCACTTGCTTTGCGAACTGCAACAAATGGGCATTGTATTGACATTTATT
CATGTGCACTTGATCAAACTGGTTTGATGGAAATGAAGCAATGTTGTAATTCAACTGGTG
GTCACATGGTAATGGGAGATTCATTCAATTCTTCACTATTTAAACAAACATTCCAACGTG
TCTTTGCCACTGATCCGAAAAATGATCTTAAAATGGGCTTCAATGCAACTTTAGAAGTGA
AATGTTCACGTGAACTTAAAATTGAAGGTGGCATTGGTCCTTGTGTATCTTTGAATGTTA
AAAATGCATCAGTTTCTGAAAATGAAGTTGGAATGGGTAATACTACTCAATGGAAATTAT
GCACAATATCACCCAATTCAACAATGGCGTTGTTCTTTGAAGTTGCTAATCAGCATTCTG
CTCCTATACCTCAGGGTGGACGAGGTTGCATTCAATTCATAACTCAATATCAACATTCGA
GTGGACAAAGAAGAATTCGTGTCACAACTGTCGCTAGAAATTGGGCAGATGCAACTGTTA
ACTTGAACTTTATTTCGGCTGGTTTTGATCAAGAAGCGGCTGCAGTAATTATGGCGAGAA
TGGTCGTTTATCGTGCTGAATCAGATGATGGTCCCGATGTTTTACGTTGGATTGATCGTC
AGTTGATTCGTTTATGTCAAAAGTTTGGCGAATACAACAAGGACGATCCAAATTCATTTA
GATTGGCTGAGAACTTTAGCTTATTTCCACAATTCATTTATCATTTGAGACGTTCGCAGT
TCTTGCAAGTTTTTAATAATTCACCAGATGAAACAACATTCTATCGTCATATGTTAATGC
GAGAAGATTTGACTCAATCATTGATTATGATTCAACCAATTTTGTACAGCTACAGTTTCA
ATGGACCGCCTGAGCCTGTTTTACTTGATACATCCAGTATTCAGCCTGATAAAATCTTAT
TAATGGACACATTCTTCCAGATATTAATTTTCCATGGTGAAACAATAGCTCAATGGCGTG
CGATGAAATATCACGAAATGAAAGAATATGAAAATTTCAAACAATTGTTGCAAGCTCCAG
TTGATGATGCACAAGAGATTTTGTCAACTCGATTCCCTATGCCGCGCTATATTGACACAG
AACAAGGCGGTTCACAAGCTCGATTCTTACTCTCAAAAGTAAATCCATCGCAAACACACA
ACACGATGTATGGATATGGTGGCCAAGATGGTGGTGCACCTGTTTTGACAGACGATGTCT
CGCTTCAAGTTTTCATGGAGCATTTGAAAAAACTAGCTGTCTCATCCACAGCATAGTGTG
CGAAAAAAATATTCCGACAAAAGTACAAGAAACTTTTGAAATGGATAAAAGTTTATAAAA
AATTTTAAATTTAATTGATTCTTGTTGCAATTAGATATAAATAAAAGATTATATATATAC
A

>g191.t28 Gene=g191 Length=647
MPPVFLFVVDTCMDDEELTALKDSLSMSLSLLPSNALVGLITFGKMVQVHELCNEGCSKS
YVFRGTKDLNAKQIQDMLGIGRGGATIQQQQQQPQQRMPQQAPQPPANRFLQPLQKCDMA
LTDMLGEMQRDPWPVSQGKRPLRATGAALSIAVGLLECTYPNTAARILLFVGGPCSTGPG
QVVDDELKHPIRSHHDIHKDNAKYMKKSIKHYEALALRTATNGHCIDIYSCALDQTGLME
MKQCCNSTGGHMVMGDSFNSSLFKQTFQRVFATDPKNDLKMGFNATLEVKCSRELKIEGG
IGPCVSLNVKNASVSENEVGMGNTTQWKLCTISPNSTMALFFEVANQHSAPIPQGGRGCI
QFITQYQHSSGQRRIRVTTVARNWADATVNLNFISAGFDQEAAAVIMARMVVYRAESDDG
PDVLRWIDRQLIRLCQKFGEYNKDDPNSFRLAENFSLFPQFIYHLRRSQFLQVFNNSPDE
TTFYRHMLMREDLTQSLIMIQPILYSYSFNGPPEPVLLDTSSIQPDKILLMDTFFQILIF
HGETIAQWRAMKYHEMKEYENFKQLLQAPVDDAQEILSTRFPMPRYIDTEQGGSQARFLL
SKVNPSQTHNTMYGYGGQDGGAPVLTDDVSLQVFMEHLKKLAVSSTA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g191.t28 CDD cd11287 Sec23_C 491 611 9.49952E-84
12 g191.t28 Gene3D G3DSA:3.40.50.410 - 1 280 6.8E-125
14 g191.t28 Gene3D G3DSA:1.20.120.730 - 394 642 1.1E-121
13 g191.t28 Gene3D G3DSA:3.40.20.10 Severin 501 605 1.1E-121
11 g191.t28 MobiDBLite mobidb-lite consensus disorder prediction 84 104 -
5 g191.t28 PANTHER PTHR11141 PROTEIN TRANSPORT PROTEIN SEC23 1 646 0.0
6 g191.t28 PANTHER PTHR11141:SF7 PROTEIN TRANSPORT PROTEIN SEC23A 1 646 0.0
1 g191.t28 Pfam PF04811 Sec23/Sec24 trunk domain 1 271 2.9E-81
3 g191.t28 Pfam PF08033 Sec23/Sec24 beta-sandwich domain 282 385 1.1E-34
2 g191.t28 Pfam PF04815 Sec23/Sec24 helical domain 399 497 1.3E-28
4 g191.t28 Pfam PF00626 Gelsolin repeat 513 599 1.0E-14
10 g191.t28 SUPERFAMILY SSF53300 vWA-like 1 271 1.92E-90
7 g191.t28 SUPERFAMILY SSF81995 beta-sandwich domain of Sec23/24 290 398 8.76E-40
9 g191.t28 SUPERFAMILY SSF81811 Helical domain of Sec23/24 399 501 3.53E-48
8 g191.t28 SUPERFAMILY SSF82754 C-terminal, gelsolin-like domain of Sec23/24 502 643 1.7E-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