General information for g13359.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-splicing factor RBM22.
Parent gene
- The parent gene g13359 is located on chr_1: 29510425..29511391 (+ 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 | g13359 | g13359.t4 | TSS | g13359.t4 | 29509895 | 29509895 |
| chr_1 | g13359 | g13359.t4 | isoform | g13359.t4 | 29509989 | 29511391 |
| chr_1 | g13359 | g13359.t4 | exon | g13359.t4.exon1 | 29509989 | 29509991 |
| chr_1 | g13359 | g13359.t4 | exon | g13359.t4.exon2 | 29510057 | 29510194 |
| chr_1 | g13359 | g13359.t4 | cds | g13359.t4.CDS1 | 29510087 | 29510194 |
| chr_1 | g13359 | g13359.t4 | exon | g13359.t4.exon3 | 29510522 | 29511391 |
| chr_1 | g13359 | g13359.t4 | cds | g13359.t4.CDS2 | 29510522 | 29511391 |
| chr_1 | g13359 | g13359.t4 | TTS | g13359.t4 | 29511462 | 29511462 |
Sequences
>g13359.t4 Gene=g13359 Length=1011
GAGAAAAGTCAATAAAACTTATTTTGCTTCAAAATGGCTATGAGCAAAACAACATCTACT
TATAATCGAACGAATTGGGAAGATTCAGAGTTTCCTATATTGTGTCAAACATGTCTAGGA
GATAATCCTTATCTTCGAATGATTCAAGATGAAATCCCACAAAGTGATGTAAATAAAGAA
TATTATTTGCAAAATGTTGAAAAGCAAATGGCAATGAATGATGGACAAATGCCTGGTGGT
GGAAAAGCTCAACAAGCTTCAGATGTTTTATCTAAATTAGCTCGCACTACACCATATTAC
AAACGAAATCTTCCTCACATTTGCTCATTTTGGGTAAAAGGAGAATGTAAAAGAGGTGAA
GAGTGTCCATATAGACATGAAAAACCAAACGATGTAGACGATCCTCTCTCAGAACAAAAT
ATTCGTGATCGATATTATGGTGTTAACGATCCAGTAGCTGAAAAGTTACTTAAAAGAGCT
GCTTCATTACCTGTCCTTGAAACTCCTAGTGACAAGACAATAACTACATTATATTGTGGT
AATGTCGGTGAACATTTGACCGAAGTTGATATAAGAGATCAATTTTATCAATATGGAGAA
ATTAGAAATGTAACACTTGTGCCGAAACAACAGTGTGCTTTCGTACAGTTTACCAAACGT
TCTTCAGCTGAATTGGCAGCAGAGAAGACCTTCAATAAATTGGTTCTTGGTGGTAAAAAA
TTGAGCATACGATGGGCATACTCACAAGCAAAACAAGCCACAGCCACATCATCATCATCA
CAATTGCGGCCTCGTATTGATCCCCGTTTAGATCCTGTACCTGGACTCCCCGATTTACCA
ACACCAAACGATTATTTCAATTTGAATGCAAATGATATGATGGTTCTACCAGCGGGCGTT
AAACTTGCACAAATTCCACAACAATTTTTGCCACCCTCATTACCAAATACATCATCTGGA
ATACATTATCCTTCTATGGATCCAAGTCGATTAGGCGCACTACAAAAATAA
>g13359.t4 Gene=g13359 Length=325
MAMSKTTSTYNRTNWEDSEFPILCQTCLGDNPYLRMIQDEIPQSDVNKEYYLQNVEKQMA
MNDGQMPGGGKAQQASDVLSKLARTTPYYKRNLPHICSFWVKGECKRGEECPYRHEKPND
VDDPLSEQNIRDRYYGVNDPVAEKLLKRAASLPVLETPSDKTITTLYCGNVGEHLTEVDI
RDQFYQYGEIRNVTLVPKQQCAFVQFTKRSSAELAAEKTFNKLVLGGKKLSIRWAYSQAK
QATATSSSSQLRPRIDPRLDPVPGLPDLPTPNDYFNLNANDMMVLPAGVKLAQIPQQFLP
PSLPNTSSGIHYPSMDPSRLGALQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13359.t4 | CDD | cd12224 | RRM_RBM22 | 163 | 235 | 3.55221E-41 |
| 8 | g13359.t4 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 83 | 132 | 5.2E-7 |
| 9 | g13359.t4 | Gene3D | G3DSA:3.30.70.330 | - | 156 | 254 | 7.8E-18 |
| 13 | g13359.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 306 | 325 | - |
| 3 | g13359.t4 | PANTHER | PTHR14089 | PRE-MRNA-SPLICING FACTOR RBM22 | 3 | 40 | 3.2E-104 |
| 5 | g13359.t4 | PANTHER | PTHR14089:SF6 | PRE-MRNA-SPLICING FACTOR RBM22 | 3 | 40 | 3.2E-104 |
| 2 | g13359.t4 | PANTHER | PTHR14089 | PRE-MRNA-SPLICING FACTOR RBM22 | 39 | 322 | 3.2E-104 |
| 4 | g13359.t4 | PANTHER | PTHR14089:SF6 | PRE-MRNA-SPLICING FACTOR RBM22 | 39 | 322 | 3.2E-104 |
| 1 | g13359.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 166 | 230 | 4.3E-10 |
| 14 | g13359.t4 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 96 | 118 | 14.774 |
| 15 | g13359.t4 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 164 | 237 | 13.72 |
| 11 | g13359.t4 | SMART | SM00356 | c3hfinal6 | 91 | 117 | 3.0E-5 |
| 12 | g13359.t4 | SMART | SM00360 | rrm1_1 | 165 | 233 | 3.3E-14 |
| 7 | g13359.t4 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 95 | 116 | 2.49E-6 |
| 6 | g13359.t4 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 158 | 241 | 2.17E-18 |
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:0046872 | metal ion binding | MF |
| GO:0003723 | RNA binding | MF |
| 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