General information for g1625.t12
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.t12 | TTS | g1625.t12 | 12204643 | 12204643 |
| chr_3 | g1625 | g1625.t12 | isoform | g1625.t12 | 12204684 | 12208169 |
| chr_3 | g1625 | g1625.t12 | exon | g1625.t12.exon1 | 12204684 | 12205135 |
| chr_3 | g1625 | g1625.t12 | cds | g1625.t12.CDS1 | 12205005 | 12205135 |
| chr_3 | g1625 | g1625.t12 | exon | g1625.t12.exon2 | 12207094 | 12207264 |
| chr_3 | g1625 | g1625.t12 | cds | g1625.t12.CDS2 | 12207094 | 12207264 |
| chr_3 | g1625 | g1625.t12 | exon | g1625.t12.exon3 | 12207409 | 12207549 |
| chr_3 | g1625 | g1625.t12 | cds | g1625.t12.CDS3 | 12207409 | 12207549 |
| chr_3 | g1625 | g1625.t12 | exon | g1625.t12.exon4 | 12207782 | 12208169 |
| chr_3 | g1625 | g1625.t12 | cds | g1625.t12.CDS4 | 12207782 | 12207782 |
| chr_3 | g1625 | g1625.t12 | TSS | g1625.t12 | NA | NA |
Sequences
>g1625.t12 Gene=g1625 Length=1152
ATGTGTAAAAATCGATGTCAGTTAGGAAATTAAATAAATTTTTCAAGAAAATTGTCTTTT
TCATTTTGTAAATTTTAAAATTGAATTTTAATTATTTCATTGAATAATTTACTACAGTTT
TAATAAATAAAAAAAAATCTAAATTAATTTTAAATCAATTCTTAATTTCTACATTCAATT
GAAAAGAGCTTTTTATTAAAAATTTAATTATTTTACAAACCTAACTTCAAATATCATTTC
AACCCTGAATCATGCACATTCTTTTCGATATTTAACTTTAAAAATCAACTTAACTTATTA
TATCATAACATAAAATTAAATTTAAGAAAATATTGAGATTAAAAAATTTATTAAATCGTG
CAGTCTTTGATTATAAATTGATATAAAATGCCTCGATATCGCGAATGGGATTTAAAATGT
AAAGTTTATGTCGGTAATTTAGATCAGAGAGCAACAAAGCATCAAATTGAAGATATATTT
AGTAAATATGGCCCATTAAGAAATGTGTGGGTGGCAAGAAATCCACCAGGCTTTGCTTTT
GTTGAATTCGAGGACAACCGCGATGCAGAAGATGCGGTAAGAAATTTGGACGGAAGTCGC
GCGTGTGGTAGTCGCATTCGTGTGGAAATGTCAAGTGGCAGAACTAGACATAATCGAGGC
AGTGGCGGTTCAAGCGATAGACGTCGCAATGATCGTGGCAATCACGTTCGAGAGATAGAT
CAAGAAGTCCACGCCGATCACCACGTCGTTCAAGACGTTCACGATCACGCTCAAGAAGTG
GCGAAAGAAGCGACCGTTCTGAATCGCGTGATCGTCGTTAAAATTATTTAATTATTTTCT
TTGTGTCTTTCAAATATTTTTGTTTAATTTTTTTGATCAAACTTAAATGCATTTTATTAA
AAAACACAATTTTTATGTTCTCGTTTGTGAGAAAAATAATTTAAAAAACAGGACAAAAAA
ATTATGAATTTGAATGGTAAAAAATTTTATATGACGATAATTGAGTTACAATGAATTAAT
TAATAATTATGTTTTTTGAACTCTCTTTTGCTACTTATTTGTCTTCTTTAAATGAGTTTC
ATAAACTCACAAATGAAATAATATTTCCTATAGAAATTTTATTAACAAAACATAAAAATA
AAACACTACTAA
>g1625.t12 Gene=g1625 Length=147
MPRYREWDLKCKVYVGNLDQRATKHQIEDIFSKYGPLRNVWVARNPPGFAFVEFEDNRDA
EDAVRNLDGSRACGSRIRVEMSSGRTRHNRGSGGSSDRRRNDRGNHVREIDQEVHADHHV
VQDVHDHAQEVAKEATVLNRVIVVKII
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1625.t12 | CDD | cd12373 | RRM_SRSF3_like | 12 | 84 | 9.56528E-44 |
| 5 | g1625.t12 | Gene3D | G3DSA:3.30.70.330 | - | 4 | 114 | 3.5E-26 |
| 9 | g1625.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 103 | - |
| 8 | g1625.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 81 | 103 | - |
| 2 | g1625.t12 | PANTHER | PTHR23147:SF186 | RNA-BINDING PROTEIN 1-RELATED | 2 | 99 | 1.9E-46 |
| 3 | g1625.t12 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 2 | 99 | 1.9E-46 |
| 1 | g1625.t12 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 13 | 77 | 1.8E-19 |
| 10 | g1625.t12 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 11 | 84 | 18.035 |
| 7 | g1625.t12 | SMART | SM00360 | rrm1_1 | 12 | 80 | 7.5E-23 |
| 4 | g1625.t12 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 11 | 106 | 9.21E-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. There were no conditions that were differentially expressed