General information for g11381.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Serine/arginine-rich splicing factor 1.
Parent gene
- The parent gene g11381 is located on chr_1: 15846807..15849014 (+ 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_1 | g11381 | g11381.t3 | TSS | g11381.t3 | 15846776 | 15846776 |
| chr_1 | g11381 | g11381.t3 | isoform | g11381.t3 | 15846807 | 15848167 |
| chr_1 | g11381 | g11381.t3 | exon | g11381.t3.exon1 | 15846807 | 15847576 |
| chr_1 | g11381 | g11381.t3 | cds | g11381.t3.CDS1 | 15847317 | 15847576 |
| chr_1 | g11381 | g11381.t3 | exon | g11381.t3.exon2 | 15847644 | 15848167 |
| chr_1 | g11381 | g11381.t3 | cds | g11381.t3.CDS2 | 15847644 | 15847773 |
| chr_1 | g11381 | g11381.t3 | TTS | g11381.t3 | 15849061 | 15849061 |
Sequences
>g11381.t3 Gene=g11381 Length=1294
ATGGCTCACAGAAGTAGTGATTCAAATAACAGAATTTATGTAGGAAATTTACCACCGGAT
ATTAGATCAAAAGATGTAGAGGATCTCTTCTTTCGTTTTGGAAAGGTTTCTTTCGTAGAT
TTAAAGAATCGAAGAGGTAATTGAGCAATTTTCAAAAAATTTTCTTACAACAAAAACTTT
GCACCAAGCCGATTTGAAAAATTTATTTTTCAGGTCCACCTTTTGCATTTGTCGAATTTG
AGGATCATCGTGATGCATCGGATGCAGTCAAAGCACGTAATAACTACGATTATGATGGGT
ATGAATTTTTTTAAAAATAAATGTAAAATTTCAAAAAAATATAAACAACCCTTTTTCTAA
AAAAATAGATATAAATTGAGAGTTGAATTTCCAAGAGGAGGTGGGCCAGGATCATACAGA
GGTGGTGGAAGATCCAATAACGATCGTGGAAGTGGAAGGAGTGGTGGTAACAATAATAGA
CCAGCCGCAAGACGAAGTCAATATCGTGTTATGGTCACTGGTTTGCCTTCGAGTGGTTCA
TGGCAAGATTTAAAAGATCATATGAGAGAAGCAGGTGATGTGTGCTTTGCCGATGTTTAT
AAAGATGGGTCAGGTGTGGTCGAGTTTCTACGACACGAAGATATGAAATACGCTATAAAG
AAATTGGACGATTCGCGATTTCGATCACATGAAGGCGAGGTAGCTTACATACGTATAAAA
GAAGATAGTGGCTCATCTCATGATACTCGCAGAGACTATAGAGATGATGGTAGCTATGGC
CGTTCGCGTTCTCGTTCTCGCTCGCCATATTCGCCACGAAAACGTCGGGGTTCTCCTGTT
TATAATGAATTCAGACCACGCGCTTCTCGCAGTCGTTCACGATCTTATAATAACTATTAA
AACTATATAAACTCACATACATATATGATAGATTGCTTAACAGACATTGAGCAAATTTAT
CCACAATTTTAAAATCTTTTTTTGCTGTCCCTGTCTCATCATTACTTTTTTAAGAGAAAA
ATTGTTTAAACCTATAATAATTTTTCATAACTCCATACATTTTTTGATAACGATATAAAT
ACATTCCTTATGTCCCATTTTAAGTGTGTGTGCGTTGCGTTTGCTGTGCCATGGAAGCTC
AACATACGCGAGTAGTGTTTTTATATAATATAATTATAATATTTTAAATTTGATTTCAAA
TGTCTAATTTTTCCATTAATAATGCAAAAATTCAATAGTGATCAAATTAAGATTCGAAAA
GAAAAAAAAATTATTAATTTTTACCTAATCTAAA
>g11381.t3 Gene=g11381 Length=129
MVTGLPSSGSWQDLKDHMREAGDVCFADVYKDGSGVVEFLRHEDMKYAIKKLDDSRFRSH
EGEVAYIRIKEDSGSSHDTRRDYRDDGSYGRSRSRSRSPYSPRKRRGSPVYNEFRPRASR
SRSRSYNNY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11381.t3 | CDD | cd12601 | RRM2_SRSF1_like | 1 | 71 | 6.85127E-47 |
| 5 | g11381.t3 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 73 | 1.4E-24 |
| 8 | g11381.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 68 | 92 | - |
| 9 | g11381.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 68 | 129 | - |
| 2 | g11381.t3 | PANTHER | PTHR23147:SF59 | SERINE/ARGININE-RICH SPLICING FACTOR 9 | 1 | 113 | 9.0E-35 |
| 3 | g11381.t3 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 1 | 113 | 9.0E-35 |
| 1 | g11381.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 1 | 61 | 5.7E-11 |
| 10 | g11381.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 72 | 10.326 |
| 7 | g11381.t3 | SMART | SM00360 | rrm1_1 | 1 | 65 | 0.0021 |
| 4 | g11381.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 2 | 80 | 1.76E-19 |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
