General information for g11381.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g11381.t1 | 15846776 | 15846776 |
| chr_1 | g11381 | g11381.t1 | isoform | g11381.t1 | 15846807 | 15847773 |
| chr_1 | g11381 | g11381.t1 | exon | g11381.t1.exon1 | 15846807 | 15846942 |
| chr_1 | g11381 | g11381.t1 | cds | g11381.t1.CDS1 | 15846807 | 15846942 |
| chr_1 | g11381 | g11381.t1 | exon | g11381.t1.exon2 | 15847020 | 15847104 |
| chr_1 | g11381 | g11381.t1 | cds | g11381.t1.CDS2 | 15847020 | 15847104 |
| chr_1 | g11381 | g11381.t1 | exon | g11381.t1.exon3 | 15847175 | 15847576 |
| chr_1 | g11381 | g11381.t1 | cds | g11381.t1.CDS3 | 15847175 | 15847576 |
| chr_1 | g11381 | g11381.t1 | exon | g11381.t1.exon4 | 15847644 | 15847773 |
| chr_1 | g11381 | g11381.t1 | cds | g11381.t1.CDS4 | 15847644 | 15847773 |
| chr_1 | g11381 | g11381.t1 | TTS | g11381.t1 | 15848129 | 15848129 |
Sequences
>g11381.t1 Gene=g11381 Length=753
ATGGCTCACAGAAGTAGTGATTCAAATAACAGAATTTATGTAGGAAATTTACCACCGGAT
ATTAGATCAAAAGATGTAGAGGATCTCTTCTTTCGTTTTGGAAAGGTTTCTTTCGTAGAT
TTAAAGAATCGAAGAGGTCCACCTTTTGCATTTGTCGAATTTGAGGATCATCGTGATGCA
TCGGATGCAGTCAAAGCACGTAATAACTACGATTATGATGGATATAAATTGAGAGTTGAA
TTTCCAAGAGGAGGTGGGCCAGGATCATACAGAGGTGGTGGAAGATCCAATAACGATCGT
GGAAGTGGAAGGAGTGGTGGTAACAATAATAGACCAGCCGCAAGACGAAGTCAATATCGT
GTTATGGTCACTGGTTTGCCTTCGAGTGGTTCATGGCAAGATTTAAAAGATCATATGAGA
GAAGCAGGTGATGTGTGCTTTGCCGATGTTTATAAAGATGGGTCAGGTGTGGTCGAGTTT
CTACGACACGAAGATATGAAATACGCTATAAAGAAATTGGACGATTCGCGATTTCGATCA
CATGAAGGCGAGGTAGCTTACATACGTATAAAAGAAGATAGTGGCTCATCTCATGATACT
CGCAGAGACTATAGAGATGATGGTAGCTATGGCCGTTCGCGTTCTCGTTCTCGCTCGCCA
TATTCGCCACGAAAACGTCGGGGTTCTCCTGTTTATAATGAATTCAGACCACGCGCTTCT
CGCAGTCGTTCACGATCTTATAATAACTATTAA
>g11381.t1 Gene=g11381 Length=250
MAHRSSDSNNRIYVGNLPPDIRSKDVEDLFFRFGKVSFVDLKNRRGPPFAFVEFEDHRDA
SDAVKARNNYDYDGYKLRVEFPRGGGPGSYRGGGRSNNDRGSGRSGGNNNRPAARRSQYR
VMVTGLPSSGSWQDLKDHMREAGDVCFADVYKDGSGVVEFLRHEDMKYAIKKLDDSRFRS
HEGEVAYIRIKEDSGSSHDTRRDYRDDGSYGRSRSRSRSPYSPRKRRGSPVYNEFRPRAS
RSRSRSYNNY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11381.t1 | CDD | cd12601 | RRM2_SRSF1_like | 119 | 192 | 3.27878E-49 |
| 7 | g11381.t1 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 89 | 2.8E-24 |
| 6 | g11381.t1 | Gene3D | G3DSA:3.30.70.330 | - | 118 | 194 | 1.4E-25 |
| 11 | g11381.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 83 | 118 | - |
| 14 | g11381.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 95 | 115 | - |
| 12 | g11381.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 250 | - |
| 13 | g11381.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 213 | - |
| 3 | g11381.t1 | PANTHER | PTHR23147:SF44 | SERINE/ARGININE-RICH SPLICING FACTOR 1 | 7 | 243 | 1.9E-76 |
| 4 | g11381.t1 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 7 | 243 | 1.9E-76 |
| 1 | g11381.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 12 | 78 | 1.9E-16 |
| 2 | g11381.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 121 | 182 | 6.7E-11 |
| 16 | g11381.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 10 | 84 | 16.961 |
| 15 | g11381.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 119 | 193 | 10.787 |
| 10 | g11381.t1 | SMART | SM00360 | rrm1_1 | 11 | 80 | 5.2E-20 |
| 9 | g11381.t1 | SMART | SM00360 | rrm1_1 | 120 | 186 | 9.0E-8 |
| 5 | g11381.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 8 | 191 | 2.31E-35 |
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 transcript has been annotated with K12890 (serine/arginine-rich splicing factor 1)
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.
