General information for g6631.t43
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Serine/arginine-rich splicing factor 7.
Parent gene
- The parent gene g6631 is located on chr_2: 17874963..17881137 (- 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_2 | g6631 | g6631.t43 | TTS | g6631.t43 | 17874939 | 17874939 |
| chr_2 | g6631 | g6631.t43 | isoform | g6631.t43 | 17874963 | 17876635 |
| chr_2 | g6631 | g6631.t43 | exon | g6631.t43.exon1 | 17874963 | 17876173 |
| chr_2 | g6631 | g6631.t43 | cds | g6631.t43.CDS1 | 17876005 | 17876173 |
| chr_2 | g6631 | g6631.t43 | exon | g6631.t43.exon2 | 17876230 | 17876408 |
| chr_2 | g6631 | g6631.t43 | cds | g6631.t43.CDS2 | 17876230 | 17876408 |
| chr_2 | g6631 | g6631.t43 | exon | g6631.t43.exon3 | 17876633 | 17876635 |
| chr_2 | g6631 | g6631.t43 | cds | g6631.t43.CDS3 | 17876633 | 17876635 |
| chr_2 | g6631 | g6631.t43 | TSS | g6631.t43 | 17876690 | 17876690 |
Sequences
>g6631.t43 Gene=g6631 Length=1393
ATGTCAAAGTCAAATAAAATGTCTCGATACCCTCACGATGCCAAAGTTTATGTTGGCGAT
TTGGGATCGAATGCAGATAAGCAGGAAATTGAAGATGCATTTAGCTACTATGGACCATTA
AGATCAGTTTGGGTAGCGAGAAACCCCCCAGGATTCGCTTTCGTAGAATTTGAAGATGCT
CGTGATGCCGAAGATTCAGTTAGAGGATTAGATGGTCGAACAATTTGTGGACGCCGAGCA
AGAGTTGAATTGTCAACTGGCAAATCAGCACGCGGATTTCGTTCTAGAGGTGGCCGTGGG
CGTTCACCTAATCGTCGAGAAGATCGCTGTTACGAATGTGGAAATAGGTAAATAAATCGA
CATTTACTTTATAAAAAATTATAAATTTATTTTATATATTAGAGGTCATTTTGCTCGTGA
TTGTCGTCGGCGTAATGGAGGAGGAAGTCGTCGTGGTGGCAGGTAATTATGTCGTTTTAT
TCTTATTTTCTTGCAGGATATTTTCGTTAAAAGAAAGAAGAGAAGAGATAACATCTTTAG
AGATAGGTTGAAAGAAAGATCTCATCAACATGAAATGACGAGATGTCCATGTATAAGTTA
GAGATAATATAATATATGCATGGGAGTAGGAAAGAGATCGACTAACGTACCATTTTCACC
AGCCGTGCCACCACAGCGTAGTATTTCTTTTGTATCAACTGAAAGAACAAGAGATGTTTT
TTTTCCATGAAATAAGAGTTTAACGTATTAACAGAAAATAAGTAATCATGATGCATCGTC
TATTGTACAGAGAGTATCAAGTATTAATGAACACACGAACAATTTATCATCTTATCTTCG
TTTCGACAAATTCGACTTCTACCTACTACTACTTTTAAATGATGACCAGACAATCGTTTA
ATCTTTTAATGATAGACATTCCCTTATTTATTATTTTTTATCGTAAATACTAAAAATGCT
CTAGAATTATTTTATTTATGTTTTATTATAATTTCTAATTTCATATTACACATAAATGTC
CCTATATCATTATCAACAACAAAAAATGAAATCAGTTAACATATAAGTACAAGACATTAC
GACACATGAAACTAATTTAATCATCGTGCGTAATCATCTTAAACGTGTGGTACATTGAGC
TGGGGTTTTAAAAGCAAGTGCACAAATTCTGTCGTAAAAGAATTATCTGAATCGAACATT
GATCACCTTTCTAAGAAAGCAATCGGCACAACTTGTAAAATTACGAGTCAACTCGAAAGT
ATGAGTAAAGATGAAGAATTTTTGTTCCTACTTCTTCTTATCCCCTTGGCTTCATGAACG
TGTCTCTTCTCGTGTGTGATATCAAGTTGAGAAACGGTAAACATGTTTCATCGCAGTGCT
TTTCTTCCATCAC
>g6631.t43 Gene=g6631 Length=116
MSKSNKMSRYPHDAKVYVGDLGSNADKQEIEDAFSYYGPLRSVWVARNPPGFAFVEFEDA
RDAEDSVRGLDGRTICGRRARVELSTGKSARGFRSRGGRGRSPNRREDRCYECGNR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6631.t43 | CDD | cd12373 | RRM_SRSF3_like | 15 | 87 | 1.14862E-43 |
| 5 | g6631.t43 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 112 | 1.8E-23 |
| 8 | g6631.t43 | MobiDBLite | mobidb-lite | consensus disorder prediction | 87 | 116 | - |
| 9 | g6631.t43 | MobiDBLite | mobidb-lite | consensus disorder prediction | 100 | 116 | - |
| 2 | g6631.t43 | PANTHER | PTHR23147:SF52 | SERINE AND ARGININE-RICH-SPLICING FACTOR 7A | 3 | 116 | 6.0E-40 |
| 3 | g6631.t43 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 3 | 116 | 6.0E-40 |
| 1 | g6631.t43 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 16 | 79 | 2.3E-17 |
| 10 | g6631.t43 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 14 | 87 | 17.063 |
| 7 | g6631.t43 | SMART | SM00360 | rrm1_1 | 15 | 83 | 3.6E-20 |
| 4 | g6631.t43 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 11 | 111 | 1.88E-26 |
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 K12896 (serine/arginine-rich splicing factor 7)
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.
