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.t1 TTS g191.t1 1634353 1634353
chr_3 g191 g191.t1 isoform g191.t1 1634566 1637197
chr_3 g191 g191.t1 exon g191.t1.exon1 1634566 1636608
chr_3 g191 g191.t1 cds g191.t1.CDS1 1634566 1636608
chr_3 g191 g191.t1 exon g191.t1.exon2 1636672 1636970
chr_3 g191 g191.t1 cds g191.t1.CDS2 1636672 1636970
chr_3 g191 g191.t1 exon g191.t1.exon3 1637098 1637106
chr_3 g191 g191.t1 cds g191.t1.CDS3 1637098 1637106
chr_3 g191 g191.t1 exon g191.t1.exon4 1637170 1637197
chr_3 g191 g191.t1 cds g191.t1.CDS4 1637170 1637197
chr_3 g191 g191.t1 TSS g191.t1 1637210 1637210

Sequences

>g191.t1 Gene=g191 Length=2379
ATGTACTTTCTCTCCACAAGTTCCAAGTCAAGATTTTTAAAATTAATTGACAACATTATG
GCAACATACGAAGAATATATTCAACAGAATGAAGATCGTGATGGAATTCGCTTTACGTGG
AACGTTTGGCCCTCGAGCCGTGTTGATGCAACTAAATTAGTTGTGCCTCTTGCTTGCTTG
TATCAACCATTTAAAGAACGAAATGATTTGCCACCAATTATGTATGAGCCTGTCTTGTGT
ACGAGAACTACATGTCGTGCTATTTTAAATCCTATGTGTCAAGTTGATTATCGTGCAAAA
TTGTGGGTCTGTAACTTTTGTTTTCAACGTAATCCTTTTCCACCACAATATGCTGCAATT
TCTGAGCAGCATCAACCAGCTGAATTAATACCTGGTTTTAGTACAATTGAGTACACTATT
ACTCGTGCACCATGTATGCCTCCAGTTTTTCTGTTCGTAGTCGATACTTGTATGGATGAT
GAAGAACTAACAGCCTTGAAAGATTCACTTTCAATGTCATTAAGTTTATTGCCTTCAAAT
GCACTTGTTGGATTAATTACTTTTGGTAAAATGGTTCAAGTTCATGAGCTTTGCAATGAA
GGATGCTCGAAAAGTTATGTTTTTCGTGGCACAAAAGATTTGAATGCTAAGCAAATTCAA
GATATGCTTGGAATTGGAAGAGGTGGTGCTACTATACAACAACAACAGCAGCAACCTCAA
CAAAGGATGCCACAACAGGCACCTCAACCACCAGCAAACAGGTTTTTGCAGCCGTTACAA
AAGTGTGACATGGCATTGACTGATATGTTGGGTGAAATGCAACGCGATCCTTGGCCTGTA
TCTCAAGGCAAACGTCCATTGAGAGCAACTGGTGCGGCTCTTTCAATTGCAGTTGGTTTA
TTGGAGTGTACTTATCCAAATACAGCTGCACGCATTTTACTTTTTGTTGGTGGTCCTTGT
TCAACAGGTCCTGGACAAGTCGTTGATGATGAATTAAAACATCCAATTCGTTCTCATCAT
GATATTCATAAAGATAATGCAAAATATATGAAAAAAAGTATCAAGCATTATGAAGCACTT
GCTTTGCGAACTGCAACAAATGGGCATTGTATTGACATTTATTCATGTGCACTTGATCAA
ACTGGTTTGATGGAAATGAAGCAATGTTGTAATTCAACTGGTGGTCACATGGTAATGGGA
GATTCATTCAATTCTTCACTATTTAAACAAACATTCCAACGTGTCTTTGCCACTGATCCG
AAAAATGATCTTAAAATGGGCTTCAATGCAACTTTAGAAGTGAAATGTTCACGTGAACTT
AAAATTGAAGGTGGCATTGGTCCTTGTGTATCTTTGAATGTTAAAAATGCATCAGTTTCT
GAAAATGAAGTTGGAATGGGTAATACTACTCAATGGAAATTATGCACAATATCACCCAAT
TCAACAATGGCGTTGTTCTTTGAAGTTGCTAATCAGCATTCTGCTCCTATACCTCAGGGT
GGACGAGGTTGCATTCAATTCATAACTCAATATCAACATTCGAGTGGACAAAGAAGAATT
CGTGTCACAACTGTCGCTAGAAATTGGGCAGATGCAACTGTTAACTTGAACTTTATTTCG
GCTGGTTTTGATCAAGAAGCGGCTGCAGTAATTATGGCGAGAATGGTCGTTTATCGTGCT
GAATCAGATGATGGTCCCGATGTTTTACGTTGGATTGATCGTCAGTTGATTCGTTTATGT
CAAAAGTTTGGCGAATACAACAAGGACGATCCAAATTCATTTAGATTGGCTGAGAACTTT
AGCTTATTTCCACAATTCATTTATCATTTGAGACGTTCGCAGTTCTTGCAAGTTTTTAAT
AATTCACCAGATGAAACAACATTCTATCGTCATATGTTAATGCGAGAAGATTTGACTCAA
TCATTGATTATGATTCAACCAATTTTGTACAGCTACAGTTTCAATGGACCGCCTGAGCCT
GTTTTACTTGATACATCCAGTATTCAGCCTGATAAAATCTTATTAATGGACACATTCTTC
CAGATATTAATTTTCCATGGTGAAACAATAGCTCAATGGCGTGCGATGAAATATCACGAA
ATGAAAGAATATGAAAATTTCAAACAATTGTTGCAAGCTCCAGTTGATGATGCACAAGAG
ATTTTGTCAACTCGATTCCCTATGCCGCGCTATATTGACACAGAACAAGGCGGTTCACAA
GCTCGATTCTTACTCTCAAAAGTAAATCCATCGCAAACACACAACACGATGTATGGATAT
GGTGGCCAAGATGGTGGTGCACCTGTTTTGACAGACGATGTCTCGCTTCAAGTTTTCATG
GAGCATTTGAAAAAACTAGCTGTCTCATCCACAGCATAG

>g191.t1 Gene=g191 Length=792
MYFLSTSSKSRFLKLIDNIMATYEEYIQQNEDRDGIRFTWNVWPSSRVDATKLVVPLACL
YQPFKERNDLPPIMYEPVLCTRTTCRAILNPMCQVDYRAKLWVCNFCFQRNPFPPQYAAI
SEQHQPAELIPGFSTIEYTITRAPCMPPVFLFVVDTCMDDEELTALKDSLSMSLSLLPSN
ALVGLITFGKMVQVHELCNEGCSKSYVFRGTKDLNAKQIQDMLGIGRGGATIQQQQQQPQ
QRMPQQAPQPPANRFLQPLQKCDMALTDMLGEMQRDPWPVSQGKRPLRATGAALSIAVGL
LECTYPNTAARILLFVGGPCSTGPGQVVDDELKHPIRSHHDIHKDNAKYMKKSIKHYEAL
ALRTATNGHCIDIYSCALDQTGLMEMKQCCNSTGGHMVMGDSFNSSLFKQTFQRVFATDP
KNDLKMGFNATLEVKCSRELKIEGGIGPCVSLNVKNASVSENEVGMGNTTQWKLCTISPN
STMALFFEVANQHSAPIPQGGRGCIQFITQYQHSSGQRRIRVTTVARNWADATVNLNFIS
AGFDQEAAAVIMARMVVYRAESDDGPDVLRWIDRQLIRLCQKFGEYNKDDPNSFRLAENF
SLFPQFIYHLRRSQFLQVFNNSPDETTFYRHMLMREDLTQSLIMIQPILYSYSFNGPPEP
VLLDTSSIQPDKILLMDTFFQILIFHGETIAQWRAMKYHEMKEYENFKQLLQAPVDDAQE
ILSTRFPMPRYIDTEQGGSQARFLLSKVNPSQTHNTMYGYGGQDGGAPVLTDDVSLQVFM
EHLKKLAVSSTA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g191.t1 CDD cd11287 Sec23_C 636 756 4.59075E-82
17 g191.t1 Gene3D G3DSA:2.60.40.1670 - 33 526 7.1E-217
18 g191.t1 Gene3D G3DSA:2.30.30.380 - 74 135 7.1E-217
14 g191.t1 Gene3D G3DSA:3.40.50.410 - 147 426 7.1E-217
16 g191.t1 Gene3D G3DSA:1.20.120.730 - 539 787 1.7E-121
15 g191.t1 Gene3D G3DSA:3.40.20.10 Severin 646 750 1.7E-121
13 g191.t1 MobiDBLite mobidb-lite consensus disorder prediction 229 249 -
6 g191.t1 PANTHER PTHR11141 PROTEIN TRANSPORT PROTEIN SEC23 20 791 0.0
7 g191.t1 PANTHER PTHR11141:SF7 PROTEIN TRANSPORT PROTEIN SEC23A 20 791 0.0
1 g191.t1 Pfam PF04810 Sec23/Sec24 zinc finger 77 117 2.0E-15
2 g191.t1 Pfam PF04811 Sec23/Sec24 trunk domain 146 416 3.4E-81
4 g191.t1 Pfam PF08033 Sec23/Sec24 beta-sandwich domain 427 530 1.4E-34
3 g191.t1 Pfam PF04815 Sec23/Sec24 helical domain 544 642 1.8E-28
5 g191.t1 Pfam PF00626 Gelsolin repeat 658 744 1.4E-14
8 g191.t1 SUPERFAMILY SSF81995 beta-sandwich domain of Sec23/24 27 543 1.13E-65
10 g191.t1 SUPERFAMILY SSF82919 Zn-finger domain of Sec23/24 66 148 2.09E-20
12 g191.t1 SUPERFAMILY SSF53300 vWA-like 146 416 4.08E-90
11 g191.t1 SUPERFAMILY SSF81811 Helical domain of Sec23/24 544 646 4.84E-48
9 g191.t1 SUPERFAMILY SSF82754 C-terminal, gelsolin-like domain of Sec23/24 647 788 2.38E-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:0008270 zinc ion binding MF
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