General information for g1625.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA-binding protein 1.
Parent gene
- The parent gene g1625 is located on chr_3: 12207773..12208169 (- 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_3 | g1625 | g1625.t1 | TTS | g1625.t1 | 12204643 | 12204643 |
| chr_3 | g1625 | g1625.t1 | isoform | g1625.t1 | 12205015 | 12208169 |
| chr_3 | g1625 | g1625.t1 | exon | g1625.t1.exon1 | 12205015 | 12205135 |
| chr_3 | g1625 | g1625.t1 | cds | g1625.t1.CDS1 | 12205015 | 12205135 |
| chr_3 | g1625 | g1625.t1 | exon | g1625.t1.exon2 | 12207081 | 12207264 |
| chr_3 | g1625 | g1625.t1 | cds | g1625.t1.CDS2 | 12207081 | 12207264 |
| chr_3 | g1625 | g1625.t1 | exon | g1625.t1.exon3 | 12207409 | 12207549 |
| chr_3 | g1625 | g1625.t1 | cds | g1625.t1.CDS3 | 12207409 | 12207549 |
| chr_3 | g1625 | g1625.t1 | exon | g1625.t1.exon4 | 12208154 | 12208169 |
| chr_3 | g1625 | g1625.t1 | cds | g1625.t1.CDS4 | 12208154 | 12208169 |
| chr_3 | g1625 | g1625.t1 | TSS | g1625.t1 | NA | NA |
Sequences
>g1625.t1 Gene=g1625 Length=462
ATGTGTAAAAATCGATTGCCTCGATATCGCGAATGGGATTTAAAATGTAAAGTTTATGTC
GGTAATTTAGATCAGAGAGCAACAAAGCATCAAATTGAAGATATATTTAGTAAATATGGC
CCATTAAGAAATGTGTGGGTGGCAAGAAATCCACCAGGCTTTGCTTTTGTTGAATTCGAG
GACAACCGCGATGCAGAAGATGCGGTAAGAAATTTGGACGGAAGTCGCGCGTGTGGTAGT
CGCATTCGTGTGGAAATGTCAAGTGGCAGAACTAGACATAATCGAGGCAGTGGCGGTTCA
AGCGATAGACGTCGCAATGATCGTGGCAGTGGAAGATACAGATCACGTTCGAGAGATAGA
TCAAGAAGTCCACGCCGATCACCACGTCGTTCAAGACGTTCACGATCACGCTCAAGAAGT
GGCGAAAGAAGCGACCGTTCTGAATCGCGTGATCGTCGTTAA
>g1625.t1 Gene=g1625 Length=153
MCKNRLPRYREWDLKCKVYVGNLDQRATKHQIEDIFSKYGPLRNVWVARNPPGFAFVEFE
DNRDAEDAVRNLDGSRACGSRIRVEMSSGRTRHNRGSGGSSDRRRNDRGSGRYRSRSRDR
SRSPRRSPRRSRRSRSRSRSGERSDRSESRDRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1625.t1 | CDD | cd12373 | RRM_SRSF3_like | 17 | 89 | 6.68283E-42 |
| 5 | g1625.t1 | Gene3D | G3DSA:3.30.70.330 | - | 9 | 122 | 4.6E-26 |
| 10 | g1625.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 153 | - |
| 8 | g1625.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 86 | 117 | - |
| 11 | g1625.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 137 | - |
| 9 | g1625.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 138 | 153 | - |
| 2 | g1625.t1 | PANTHER | PTHR23147:SF186 | RNA-BINDING PROTEIN 1-RELATED | 7 | 142 | 2.5E-47 |
| 3 | g1625.t1 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 7 | 142 | 2.5E-47 |
| 1 | g1625.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 18 | 82 | 2.0E-19 |
| 12 | g1625.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 16 | 89 | 18.035 |
| 7 | g1625.t1 | SMART | SM00360 | rrm1_1 | 17 | 85 | 7.5E-23 |
| 4 | g1625.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 16 | 118 | 1.34E-28 |
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.
