General information for g6631.t28
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.t28 | isoform | g6631.t28 | 17873971 | 17881137 |
| chr_2 | g6631 | g6631.t28 | exon | g6631.t28.exon1 | 17873971 | 17874102 |
| chr_2 | g6631 | g6631.t28 | cds | g6631.t28.CDS1 | 17873976 | 17874102 |
| chr_2 | g6631 | g6631.t28 | TTS | g6631.t28 | 17873978 | 17873978 |
| chr_2 | g6631 | g6631.t28 | exon | g6631.t28.exon2 | 17874162 | 17874285 |
| chr_2 | g6631 | g6631.t28 | cds | g6631.t28.CDS2 | 17874162 | 17874285 |
| chr_2 | g6631 | g6631.t28 | exon | g6631.t28.exon3 | 17874357 | 17874502 |
| chr_2 | g6631 | g6631.t28 | cds | g6631.t28.CDS3 | 17874357 | 17874502 |
| chr_2 | g6631 | g6631.t28 | exon | g6631.t28.exon4 | 17875894 | 17875953 |
| chr_2 | g6631 | g6631.t28 | cds | g6631.t28.CDS4 | 17875894 | 17875953 |
| chr_2 | g6631 | g6631.t28 | exon | g6631.t28.exon5 | 17876009 | 17876173 |
| chr_2 | g6631 | g6631.t28 | cds | g6631.t28.CDS5 | 17876009 | 17876173 |
| chr_2 | g6631 | g6631.t28 | exon | g6631.t28.exon6 | 17876230 | 17876408 |
| chr_2 | g6631 | g6631.t28 | cds | g6631.t28.CDS6 | 17876230 | 17876408 |
| chr_2 | g6631 | g6631.t28 | exon | g6631.t28.exon7 | 17881088 | 17881137 |
| chr_2 | g6631 | g6631.t28 | cds | g6631.t28.CDS7 | 17881088 | 17881090 |
| chr_2 | g6631 | g6631.t28 | TSS | g6631.t28 | NA | NA |
Sequences
>g6631.t28 Gene=g6631 Length=856
TAATAGGCGAGCGAAAGAAAACTGAAGCTCGTAATTTATTTTCGGAAATGTCAAAGTCAA
ATAAAATGTCTCGATACCCTCACGATGCCAAAGTTTATGTTGGCGATTTGGGATCGAATG
CAGATAAGCAGGAAATTGAAGATGCATTTAGCTACTATGGACCATTAAGATCAGTTTGGG
TAGCGAGAAACCCCCCAGGATTCGCTTTCGTAGAATTTGAAGATGCTCGTGATGCCGAAG
ATTCAGTTAGAGGATTAGATGGTCGAACAATTTGTGGACGCCGAGCAAGAGTTGAATTGT
CAACTGGCAAATCAGCACGCGGATTTCGTTCTAGAGGTGGCCGTGGGCGTTCACCTAATC
GTCGAGAAGATCGCTGTTACGAATGTGGAAATAGAGGTCATTTTGCTCGTGATTGTCGTC
GGCGTAATGGAGGAGGAAGTCGTCGTGGTGGCAGATCTCGAAGCCGCTCTCGATCGCGTA
GATCTCGTAGTCACTCGAGAGATCATAGATACAGTCGTTCACCAGCAGATCGAACAAGAG
ATCGCAGATCTCATTCAAGCGACCGTAGATCTGCTTCTGAACTTAGCGAAACACGAAAAA
TGACAAGTCATGGAAGAGTTCAAGGACAAATTCACCACAGTCAGATAGATCTCGAAGAAG
TCGTTCCCAAGACACTCAAGCCTCCAATTCGGAACCGCGTAAAGAGTGAAATGAGATTCA
TTCCGTTGGTAGTTACATCTTTAAGAACATCTAATAATTGCCGTATGACTTACGAGAAAA
GTGACCTATTCATCAGTCATACATTATATAATATAAATTATAGTTTGAATAAATTGATTT
ATATTATATAAAAAAA
>g6631.t28 Gene=g6631 Length=267
MSKSNKMSRYPHDAKVYVGDLGSNADKQEIEDAFSYYGPLRSVWVARNPPGFAFVEFEDA
RDAEDSVRGLDGRTICGRRARVELSTGKSARGFRSRGGRGRSPNRREDRCYECGNRGHFA
RDCRRRNGGGSRRGGRSRSRSRSRRSRSHSRDHRYSRSPADRTRDRRSHSSDRRSASELS
ETRKMTSHGRVQGQIHHSQIDLEEVVPKTLKPPIRNRVKSEMRFIPLVVTSLRTSNNCRM
TYEKSDLFISHTLYNINYSLNKLIYII
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6631.t28 | CDD | cd12373 | RRM_SRSF3_like | 15 | 87 | 9.00791E-46 |
| 7 | g6631.t28 | Gene3D | G3DSA:3.30.70.330 | - | 7 | 88 | 1.9E-22 |
| 6 | g6631.t28 | Gene3D | G3DSA:4.10.60.10 | - | 89 | 139 | 2.6E-7 |
| 13 | g6631.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 87 | 107 | - |
| 11 | g6631.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 124 | 200 | - |
| 14 | g6631.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 130 | 152 | - |
| 12 | g6631.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 153 | 185 | - |
| 3 | g6631.t28 | PANTHER | PTHR23147:SF52 | SERINE AND ARGININE-RICH-SPLICING FACTOR 7A | 3 | 161 | 1.7E-47 |
| 4 | g6631.t28 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 3 | 161 | 1.7E-47 |
| 2 | g6631.t28 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 16 | 79 | 1.4E-16 |
| 1 | g6631.t28 | Pfam | PF00098 | Zinc knuckle | 109 | 124 | 2.2E-5 |
| 16 | g6631.t28 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 14 | 87 | 17.063 |
| 15 | g6631.t28 | ProSiteProfiles | PS50158 | Zinc finger CCHC-type profile. | 109 | 125 | 10.79 |
| 10 | g6631.t28 | SMART | SM00360 | rrm1_1 | 15 | 83 | 3.6E-20 |
| 9 | g6631.t28 | SMART | SM00343 | c2hcfinal6 | 109 | 125 | 0.0017 |
| 5 | g6631.t28 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 11 | 115 | 1.33E-25 |
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:0008270 | zinc ion binding | MF |
| 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. There were no conditions that were differentially expressed