General information for g6631.t18
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.t18 | isoform | g6631.t18 | 17873971 | 17876635 |
| chr_2 | g6631 | g6631.t18 | exon | g6631.t18.exon1 | 17873971 | 17874102 |
| chr_2 | g6631 | g6631.t18 | TTS | g6631.t18 | 17873978 | 17873978 |
| chr_2 | g6631 | g6631.t18 | exon | g6631.t18.exon2 | 17874162 | 17874295 |
| chr_2 | g6631 | g6631.t18 | cds | g6631.t18.CDS1 | 17874286 | 17874295 |
| chr_2 | g6631 | g6631.t18 | exon | g6631.t18.exon3 | 17874353 | 17874502 |
| chr_2 | g6631 | g6631.t18 | cds | g6631.t18.CDS2 | 17874353 | 17874502 |
| chr_2 | g6631 | g6631.t18 | exon | g6631.t18.exon4 | 17875894 | 17875953 |
| chr_2 | g6631 | g6631.t18 | cds | g6631.t18.CDS3 | 17875894 | 17875953 |
| chr_2 | g6631 | g6631.t18 | exon | g6631.t18.exon5 | 17876009 | 17876173 |
| chr_2 | g6631 | g6631.t18 | cds | g6631.t18.CDS4 | 17876009 | 17876173 |
| chr_2 | g6631 | g6631.t18 | exon | g6631.t18.exon6 | 17876230 | 17876408 |
| chr_2 | g6631 | g6631.t18 | cds | g6631.t18.CDS5 | 17876230 | 17876408 |
| chr_2 | g6631 | g6631.t18 | exon | g6631.t18.exon7 | 17876633 | 17876635 |
| chr_2 | g6631 | g6631.t18 | cds | g6631.t18.CDS6 | 17876633 | 17876635 |
| chr_2 | g6631 | g6631.t18 | TSS | g6631.t18 | 17876690 | 17876690 |
Sequences
>g6631.t18 Gene=g6631 Length=823
ATGTCAAAGTCAAATAAAATGTCTCGATACCCTCACGATGCCAAAGTTTATGTTGGCGAT
TTGGGATCGAATGCAGATAAGCAGGAAATTGAAGATGCATTTAGCTACTATGGACCATTA
AGATCAGTTTGGGTAGCGAGAAACCCCCCAGGATTCGCTTTCGTAGAATTTGAAGATGCT
CGTGATGCCGAAGATTCAGTTAGAGGATTAGATGGTCGAACAATTTGTGGACGCCGAGCA
AGAGTTGAATTGTCAACTGGCAAATCAGCACGCGGATTTCGTTCTAGAGGTGGCCGTGGG
CGTTCACCTAATCGTCGAGAAGATCGCTGTTACGAATGTGGAAATAGAGGTCATTTTGCT
CGTGATTGTCGTCGGCGTAATGGAGGAGGAAGTCGTCGTGGTGGCAGATCTCGAAGCCGC
TCTCGATCGCGTAGATCTCGTAGTCACTCGAGAGATCATAGATACAGTCGTTCACCAGCA
GATCGAACAAGAGATCGCAGATCTCATTCAAGCGACCGTAGATCTGCTTCTGAACTTAGC
GAAACACGAAAAAGTAAAAAAACATAGTGACAAGTCATGGAAGAGTTCAAGGACAAATTC
ACCACAGTCAGATAGATCTCGAAGAAGTCGTTCCCAAGACACTCAAGCCTCCAATTCGGA
ACCGCGTAAAGAGTGAAATGAGATTCATTCCGTTGGTAGTTACATCTTTAAGAACATCTA
ATAATTGCCGTATGACTTACGAGAAAAGTGACCTATTCATCAGTCATACATTATATAATA
TAAATTATAGTTTGAATAAATTGATTTATATTATATAAAAAAA
>g6631.t18 Gene=g6631 Length=188
MSKSNKMSRYPHDAKVYVGDLGSNADKQEIEDAFSYYGPLRSVWVARNPPGFAFVEFEDA
RDAEDSVRGLDGRTICGRRARVELSTGKSARGFRSRGGRGRSPNRREDRCYECGNRGHFA
RDCRRRNGGGSRRGGRSRSRSRSRRSRSHSRDHRYSRSPADRTRDRRSHSSDRRSASELS
ETRKSKKT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6631.t18 | CDD | cd12373 | RRM_SRSF3_like | 15 | 87 | 5.15224E-43 |
| 7 | g6631.t18 | Gene3D | G3DSA:3.30.70.330 | - | 7 | 88 | 9.2E-23 |
| 6 | g6631.t18 | Gene3D | G3DSA:4.10.60.10 | - | 89 | 135 | 4.3E-8 |
| 11 | g6631.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 84 | 107 | - |
| 14 | g6631.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 124 | 188 | - |
| 12 | g6631.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 130 | 152 | - |
| 13 | g6631.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 153 | 188 | - |
| 3 | g6631.t18 | PANTHER | PTHR23147:SF52 | SERINE AND ARGININE-RICH-SPLICING FACTOR 7A | 3 | 158 | 2.3E-44 |
| 4 | g6631.t18 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 3 | 158 | 2.3E-44 |
| 2 | g6631.t18 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 16 | 79 | 7.2E-17 |
| 1 | g6631.t18 | Pfam | PF00098 | Zinc knuckle | 109 | 124 | 1.4E-5 |
| 16 | g6631.t18 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 14 | 87 | 17.063 |
| 15 | g6631.t18 | ProSiteProfiles | PS50158 | Zinc finger CCHC-type profile. | 109 | 125 | 10.79 |
| 10 | g6631.t18 | SMART | SM00360 | rrm1_1 | 15 | 83 | 3.6E-20 |
| 9 | g6631.t18 | SMART | SM00343 | c2hcfinal6 | 109 | 125 | 0.0017 |
| 5 | g6631.t18 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 11 | 115 | 5.57E-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: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