Gene loci information

Transcript annotation

  • This transcript has been annotated as Pre-mRNA-splicing factor RBM22.

Parent gene

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.t13 TSS g13359.t13 29509895 29509895
chr_1 g13359 g13359.t13 isoform g13359.t13 29510425 29511391
chr_1 g13359 g13359.t13 exon g13359.t13.exon1 29510425 29511391
chr_1 g13359 g13359.t13 cds g13359.t13.CDS1 29510588 29511391
chr_1 g13359 g13359.t13 TTS g13359.t13 29511462 29511462

Sequences

>g13359.t13 Gene=g13359 Length=967
ATTTTTGAAATTTGAAAAACCTTTTATTTGTTCATTTAAAATTACAATTTATTAAATTTC
AGGATTACCGACTCAAGTGCGAGATACAGCACTCAAAATTCAAGATGAAATCCCACAAAG
TGATGTAAATAAAGAATATTATTTGCAAAATGTTGAAAAGCAAATGGCAATGAATGATGG
ACAAATGCCTGGTGGTGGAAAAGCTCAACAAGCTTCAGATGTTTTATCTAAATTAGCTCG
CACTACACCATATTACAAACGAAATCTTCCTCACATTTGCTCATTTTGGGTAAAAGGAGA
ATGTAAAAGAGGTGAAGAGTGTCCATATAGACATGAAAAACCAAACGATGTAGACGATCC
TCTCTCAGAACAAAATATTCGTGATCGATATTATGGTGTTAACGATCCAGTAGCTGAAAA
GTTACTTAAAAGAGCTGCTTCATTACCTGTCCTTGAAACTCCTAGTGACAAGACAATAAC
TACATTATATTGTGGTAATGTCGGTGAACATTTGACCGAAGTTGATATAAGAGATCAATT
TTATCAATATGGAGAAATTAGAAATGTAACACTTGTGCCGAAACAACAGTGTGCTTTCGT
ACAGTTTACCAAACGTTCTTCAGCTGAATTGGCAGCAGAGAAGACCTTCAATAAATTGGT
TCTTGGTGGTAAAAAATTGAGCATACGATGGGCATACTCACAAGCAAAACAAGCCACAGC
CACATCATCATCATCACAATTGCGGCCTCGTATTGATCCCCGTTTAGATCCTGTACCTGG
ACTCCCCGATTTACCAACACCAAACGATTATTTCAATTTGAATGCAAATGATATGATGGT
TCTACCAGCGGGCGTTAAACTTGCACAAATTCCACAACAATTTTTGCCACCCTCATTACC
AAATACATCATCTGGAATACATTATCCTTCTATGGATCCAAGTCGATTAGGCGCACTACA
AAAATAA

>g13359.t13 Gene=g13359 Length=267
MAMNDGQMPGGGKAQQASDVLSKLARTTPYYKRNLPHICSFWVKGECKRGEECPYRHEKP
NDVDDPLSEQNIRDRYYGVNDPVAEKLLKRAASLPVLETPSDKTITTLYCGNVGEHLTEV
DIRDQFYQYGEIRNVTLVPKQQCAFVQFTKRSSAELAAEKTFNKLVLGGKKLSIRWAYSQ
AKQATATSSSSQLRPRIDPRLDPVPGLPDLPTPNDYFNLNANDMMVLPAGVKLAQIPQQF
LPPSLPNTSSGIHYPSMDPSRLGALQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13359.t13 CDD cd12224 RRM_RBM22 105 177 7.54173E-42
6 g13359.t13 Gene3D G3DSA:4.10.1000.10 CCCH zinc finger 25 74 3.9E-7
7 g13359.t13 Gene3D G3DSA:3.30.70.330 - 98 196 5.3E-18
11 g13359.t13 MobiDBLite mobidb-lite consensus disorder prediction 248 267 -
2 g13359.t13 PANTHER PTHR14089 PRE-MRNA-SPLICING FACTOR RBM22 12 264 2.1E-80
3 g13359.t13 PANTHER PTHR14089:SF6 PRE-MRNA-SPLICING FACTOR RBM22 12 264 2.1E-80
1 g13359.t13 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 108 172 3.1E-10
12 g13359.t13 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 38 60 14.774
13 g13359.t13 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 106 179 13.72
9 g13359.t13 SMART SM00356 c3hfinal6 33 59 3.0E-5
10 g13359.t13 SMART SM00360 rrm1_1 107 175 3.3E-14
5 g13359.t13 SUPERFAMILY SSF90229 CCCH zinc finger 37 58 1.83E-6
4 g13359.t13 SUPERFAMILY SSF54928 RNA-binding domain, RBD 100 184 1.36E-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.

Raw TPM values