General information for g11728.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA-binding protein with serine-rich domain 1.
Parent gene
- The parent gene g11728 is located on chr_1: 18097630..18098317 (+ 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_1 | g11728 | g11728.t4 | TSS | g11728.t4 | 18096347 | 18096347 |
| chr_1 | g11728 | g11728.t4 | isoform | g11728.t4 | 18096543 | 18097630 |
| chr_1 | g11728 | g11728.t4 | exon | g11728.t4.exon1 | 18096543 | 18096628 |
| chr_1 | g11728 | g11728.t4 | cds | g11728.t4.CDS1 | 18096543 | 18096628 |
| chr_1 | g11728 | g11728.t4 | exon | g11728.t4.exon2 | 18096678 | 18096728 |
| chr_1 | g11728 | g11728.t4 | cds | g11728.t4.CDS2 | 18096678 | 18096728 |
| chr_1 | g11728 | g11728.t4 | exon | g11728.t4.exon3 | 18096790 | 18096942 |
| chr_1 | g11728 | g11728.t4 | cds | g11728.t4.CDS3 | 18096790 | 18096942 |
| chr_1 | g11728 | g11728.t4 | exon | g11728.t4.exon4 | 18097006 | 18097294 |
| chr_1 | g11728 | g11728.t4 | cds | g11728.t4.CDS4 | 18097006 | 18097294 |
| chr_1 | g11728 | g11728.t4 | exon | g11728.t4.exon5 | 18097358 | 18097442 |
| chr_1 | g11728 | g11728.t4 | cds | g11728.t4.CDS5 | 18097358 | 18097360 |
| chr_1 | g11728 | g11728.t4 | exon | g11728.t4.exon6 | 18097507 | 18097630 |
| chr_1 | g11728 | g11728.t4 | TTS | g11728.t4 | 18097769 | 18097769 |
Sequences
>g11728.t4 Gene=g11728 Length=788
ATGGTGGTAGAAAAATCGCGTAGTGAAAAAGAAAAGGAAGAGAAATCATCTAAAAGAAGA
TCTCGTTCAACTAGTTCTAATGATAGTTCTAGTTCGGATAGTTCATCCAGCAGTAGTTCA
TCTTCTAGTTCGTCTAGTTCATCTTCAACATCATCATCAAGTAGTGGTGGTGATCGTCGT
AAACGCAGAGAAAGAGGATCTCGATCCAAAAGTCGCAGTGTGCGAAAAGGTGGTGAATCA
AAAGATAGAAAGGAGAAATCACGCGAGAGAGGACGTCAAAGTCCTGGAAGACGAACTCGT
TCCCGATCAACTTCAGTTCGACGTAAACGTTATGAACGTTCACCAACACCAAAACCTACA
CGAATTCATATAGGTCGTCTGACTCGTAATGTAACAAAGGATCATGTTCTTGAAATTTTC
AGCAACTATGGAGAGATTAAATCTATTGATTTTCCAACTGATCGTTATCATCCACAAAAT
GGTAGAGGCTTCTGTTATGTTGAATATTTAAATGCAGACGATGCTGAAAATGCTATGAAA
CACATGGACGGAGGTCAAATTGATGGAACTGAAGTTGCTTAAATAATCCAAAGCCAATGC
AAATGATGCGTCGTTCTCCTATGCGAAGAGGAGGTATGCCTCCAAATCGTAATAACAATA
GATGGAGAGGTGGTGGTAGAGATATGCAAAATCGACGCAGATCTCCGATAAGACGTTCAC
CTCGACGCAGAGTTAGTCGAAGTCCAATAAGAAGACGCCACTCTAATTCATCAAGTAGCT
CGCGTTAG
>g11728.t4 Gene=g11728 Length=193
MVVEKSRSEKEKEEKSSKRRSRSTSSNDSSSSDSSSSSSSSSSSSSSSSTSSSSSGGDRR
KRRERGSRSKSRSVRKGGESKDRKEKSRERGRQSPGRRTRSRSTSVRRKRYERSPTPKPT
RIHIGRLTRNVTKDHVLEIFSNYGEIKSIDFPTDRYHPQNGRGFCYVEYLNADDAENAMK
HMDGGQIDGTEVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11728.t4 | CDD | cd12365 | RRM_RNPS1 | 122 | 193 | 1.00982E-38 |
| 5 | g11728.t4 | Gene3D | G3DSA:3.30.70.330 | - | 117 | 193 | 8.6E-21 |
| 9 | g11728.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 118 | - |
| 10 | g11728.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 8 | g11728.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 23 | 55 | - |
| 11 | g11728.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 71 | 96 | - |
| 2 | g11728.t4 | PANTHER | PTHR15481 | RIBONUCLEIC ACID BINDING PROTEIN S1 | 5 | 192 | 1.5E-46 |
| 3 | g11728.t4 | PANTHER | PTHR15481:SF2 | RNA-BINDING PROTEIN WITH SERINE-RICH DOMAIN 1 | 5 | 192 | 1.5E-46 |
| 1 | g11728.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 123 | 192 | 4.5E-17 |
| 12 | g11728.t4 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 120 | 193 | 15.681 |
| 7 | g11728.t4 | SMART | SM00360 | rrm1_1 | 121 | 193 | 1.3E-17 |
| 4 | g11728.t4 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 114 | 191 | 5.51E-22 |
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 K14325 (RNA-binding protein with serine-rich domain 1)
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.
