General information for g191.t29
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein transport protein Sec23A.
Parent gene
- The parent gene g191 is located on chr_3: 1637197..1639086 (- 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_3 | g191 | g191.t29 | TTS | g191.t29 | 1634353 | 1634353 |
| chr_3 | g191 | g191.t29 | isoform | g191.t29 | 1634566 | 1637197 |
| chr_3 | g191 | g191.t29 | exon | g191.t29.exon1 | 1634566 | 1636608 |
| chr_3 | g191 | g191.t29 | cds | g191.t29.CDS1 | 1634566 | 1636608 |
| chr_3 | g191 | g191.t29 | exon | g191.t29.exon2 | 1636672 | 1636970 |
| chr_3 | g191 | g191.t29 | cds | g191.t29.CDS2 | 1636672 | 1636950 |
| chr_3 | g191 | g191.t29 | exon | g191.t29.exon3 | 1637098 | 1637197 |
| chr_3 | g191 | g191.t29 | TSS | g191.t29 | 1637210 | 1637210 |
Sequences
>g191.t29 Gene=g191 Length=2442
ATGTACTTTCTCTCCACAAGTTCCAAGTGTAAATTTTCATTTGGTTCAGTGTTAATTAAA
GGAAAATTAAATAAATTAAATATATAACAAGCAAGATTTTTAAAATTAATTGACAACATT
ATGGCAACATACGAAGAATATATTCAACAGAATGAAGATCGTGATGGAATTCGCTTTACG
TGGAACGTTTGGCCCTCGAGCCGTGTTGATGCAACTAAATTAGTTGTGCCTCTTGCTTGC
TTGTATCAACCATTTAAAGAACGAAATGATTTGCCACCAATTATGTATGAGCCTGTCTTG
TGTACGAGAACTACATGTCGTGCTATTTTAAATCCTATGTGTCAAGTTGATTATCGTGCA
AAATTGTGGGTCTGTAACTTTTGTTTTCAACGTAATCCTTTTCCACCACAATATGCTGCA
ATTTCTGAGCAGCATCAACCAGCTGAATTAATACCTGGTTTTAGTACAATTGAGTACACT
ATTACTCGTGCACCATGTATGCCTCCAGTTTTTCTGTTCGTAGTCGATACTTGTATGGAT
GATGAAGAACTAACAGCCTTGAAAGATTCACTTTCAATGTCATTAAGTTTATTGCCTTCA
AATGCACTTGTTGGATTAATTACTTTTGGTAAAATGGTTCAAGTTCATGAGCTTTGCAAT
GAAGGATGCTCGAAAAGTTATGTTTTTCGTGGCACAAAAGATTTGAATGCTAAGCAAATT
CAAGATATGCTTGGAATTGGAAGAGGTGGTGCTACTATACAACAACAACAGCAGCAACCT
CAACAAAGGATGCCACAACAGGCACCTCAACCACCAGCAAACAGGTTTTTGCAGCCGTTA
CAAAAGTGTGACATGGCATTGACTGATATGTTGGGTGAAATGCAACGCGATCCTTGGCCT
GTATCTCAAGGCAAACGTCCATTGAGAGCAACTGGTGCGGCTCTTTCAATTGCAGTTGGT
TTATTGGAGTGTACTTATCCAAATACAGCTGCACGCATTTTACTTTTTGTTGGTGGTCCT
TGTTCAACAGGTCCTGGACAAGTCGTTGATGATGAATTAAAACATCCAATTCGTTCTCAT
CATGATATTCATAAAGATAATGCAAAATATATGAAAAAAAGTATCAAGCATTATGAAGCA
CTTGCTTTGCGAACTGCAACAAATGGGCATTGTATTGACATTTATTCATGTGCACTTGAT
CAAACTGGTTTGATGGAAATGAAGCAATGTTGTAATTCAACTGGTGGTCACATGGTAATG
GGAGATTCATTCAATTCTTCACTATTTAAACAAACATTCCAACGTGTCTTTGCCACTGAT
CCGAAAAATGATCTTAAAATGGGCTTCAATGCAACTTTAGAAGTGAAATGTTCACGTGAA
CTTAAAATTGAAGGTGGCATTGGTCCTTGTGTATCTTTGAATGTTAAAAATGCATCAGTT
TCTGAAAATGAAGTTGGAATGGGTAATACTACTCAATGGAAATTATGCACAATATCACCC
AATTCAACAATGGCGTTGTTCTTTGAAGTTGCTAATCAGCATTCTGCTCCTATACCTCAG
GGTGGACGAGGTTGCATTCAATTCATAACTCAATATCAACATTCGAGTGGACAAAGAAGA
ATTCGTGTCACAACTGTCGCTAGAAATTGGGCAGATGCAACTGTTAACTTGAACTTTATT
TCGGCTGGTTTTGATCAAGAAGCGGCTGCAGTAATTATGGCGAGAATGGTCGTTTATCGT
GCTGAATCAGATGATGGTCCCGATGTTTTACGTTGGATTGATCGTCAGTTGATTCGTTTA
TGTCAAAAGTTTGGCGAATACAACAAGGACGATCCAAATTCATTTAGATTGGCTGAGAAC
TTTAGCTTATTTCCACAATTCATTTATCATTTGAGACGTTCGCAGTTCTTGCAAGTTTTT
AATAATTCACCAGATGAAACAACATTCTATCGTCATATGTTAATGCGAGAAGATTTGACT
CAATCATTGATTATGATTCAACCAATTTTGTACAGCTACAGTTTCAATGGACCGCCTGAG
CCTGTTTTACTTGATACATCCAGTATTCAGCCTGATAAAATCTTATTAATGGACACATTC
TTCCAGATATTAATTTTCCATGGTGAAACAATAGCTCAATGGCGTGCGATGAAATATCAC
GAAATGAAAGAATATGAAAATTTCAAACAATTGTTGCAAGCTCCAGTTGATGATGCACAA
GAGATTTTGTCAACTCGATTCCCTATGCCGCGCTATATTGACACAGAACAAGGCGGTTCA
CAAGCTCGATTCTTACTCTCAAAAGTAAATCCATCGCAAACACACAACACGATGTATGGA
TATGGTGGCCAAGATGGTGGTGCACCTGTTTTGACAGACGATGTCTCGCTTCAAGTTTTC
ATGGAGCATTTGAAAAAACTAGCTGTCTCATCCACAGCATAG
>g191.t29 Gene=g191 Length=773
MATYEEYIQQNEDRDGIRFTWNVWPSSRVDATKLVVPLACLYQPFKERNDLPPIMYEPVL
CTRTTCRAILNPMCQVDYRAKLWVCNFCFQRNPFPPQYAAISEQHQPAELIPGFSTIEYT
ITRAPCMPPVFLFVVDTCMDDEELTALKDSLSMSLSLLPSNALVGLITFGKMVQVHELCN
EGCSKSYVFRGTKDLNAKQIQDMLGIGRGGATIQQQQQQPQQRMPQQAPQPPANRFLQPL
QKCDMALTDMLGEMQRDPWPVSQGKRPLRATGAALSIAVGLLECTYPNTAARILLFVGGP
CSTGPGQVVDDELKHPIRSHHDIHKDNAKYMKKSIKHYEALALRTATNGHCIDIYSCALD
QTGLMEMKQCCNSTGGHMVMGDSFNSSLFKQTFQRVFATDPKNDLKMGFNATLEVKCSRE
LKIEGGIGPCVSLNVKNASVSENEVGMGNTTQWKLCTISPNSTMALFFEVANQHSAPIPQ
GGRGCIQFITQYQHSSGQRRIRVTTVARNWADATVNLNFISAGFDQEAAAVIMARMVVYR
AESDDGPDVLRWIDRQLIRLCQKFGEYNKDDPNSFRLAENFSLFPQFIYHLRRSQFLQVF
NNSPDETTFYRHMLMREDLTQSLIMIQPILYSYSFNGPPEPVLLDTSSIQPDKILLMDTF
FQILIFHGETIAQWRAMKYHEMKEYENFKQLLQAPVDDAQEILSTRFPMPRYIDTEQGGS
QARFLLSKVNPSQTHNTMYGYGGQDGGAPVLTDDVSLQVFMEHLKKLAVSSTA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g191.t29 | CDD | cd11287 | Sec23_C | 617 | 737 | 3.02691E-82 |
| 17 | g191.t29 | Gene3D | G3DSA:2.60.40.1670 | - | 14 | 507 | 6.6E-217 |
| 18 | g191.t29 | Gene3D | G3DSA:2.30.30.380 | - | 55 | 116 | 6.6E-217 |
| 14 | g191.t29 | Gene3D | G3DSA:3.40.50.410 | - | 128 | 407 | 6.6E-217 |
| 16 | g191.t29 | Gene3D | G3DSA:1.20.120.730 | - | 520 | 768 | 1.7E-121 |
| 15 | g191.t29 | Gene3D | G3DSA:3.40.20.10 | Severin | 627 | 731 | 1.7E-121 |
| 13 | g191.t29 | MobiDBLite | mobidb-lite | consensus disorder prediction | 210 | 230 | - |
| 6 | g191.t29 | PANTHER | PTHR11141 | PROTEIN TRANSPORT PROTEIN SEC23 | 1 | 772 | 0.0 |
| 7 | g191.t29 | PANTHER | PTHR11141:SF7 | PROTEIN TRANSPORT PROTEIN SEC23A | 1 | 772 | 0.0 |
| 1 | g191.t29 | Pfam | PF04810 | Sec23/Sec24 zinc finger | 58 | 98 | 2.0E-15 |
| 2 | g191.t29 | Pfam | PF04811 | Sec23/Sec24 trunk domain | 127 | 397 | 3.2E-81 |
| 4 | g191.t29 | Pfam | PF08033 | Sec23/Sec24 beta-sandwich domain | 408 | 511 | 1.4E-34 |
| 3 | g191.t29 | Pfam | PF04815 | Sec23/Sec24 helical domain | 525 | 623 | 1.8E-28 |
| 5 | g191.t29 | Pfam | PF00626 | Gelsolin repeat | 639 | 725 | 1.3E-14 |
| 8 | g191.t29 | SUPERFAMILY | SSF81995 | beta-sandwich domain of Sec23/24 | 8 | 524 | 1.05E-65 |
| 10 | g191.t29 | SUPERFAMILY | SSF82919 | Zn-finger domain of Sec23/24 | 47 | 129 | 2.09E-20 |
| 12 | g191.t29 | SUPERFAMILY | SSF53300 | vWA-like | 127 | 397 | 3.71E-90 |
| 11 | g191.t29 | SUPERFAMILY | SSF81811 | Helical domain of Sec23/24 | 525 | 627 | 4.71E-48 |
| 9 | g191.t29 | SUPERFAMILY | SSF82754 | C-terminal, gelsolin-like domain of Sec23/24 | 628 | 769 | 2.3E-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
- This transcript has been annotated with K14006 (protein transport protein SEC23)
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.
