Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative RNA-binding protein 25.

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_3 g568 g568.t2 TSS g568.t2 4171916 4171916
chr_3 g568 g568.t2 isoform g568.t2 4172173 4173062
chr_3 g568 g568.t2 exon g568.t2.exon1 4172173 4172229
chr_3 g568 g568.t2 cds g568.t2.CDS1 4172173 4172229
chr_3 g568 g568.t2 exon g568.t2.exon2 4172294 4172420
chr_3 g568 g568.t2 cds g568.t2.CDS2 4172294 4172420
chr_3 g568 g568.t2 exon g568.t2.exon3 4172485 4172593
chr_3 g568 g568.t2 cds g568.t2.CDS3 4172485 4172593
chr_3 g568 g568.t2 exon g568.t2.exon4 4172665 4173062
chr_3 g568 g568.t2 cds g568.t2.CDS4 4172665 4173061
chr_3 g568 g568.t2 TTS g568.t2 4173528 4173528

Sequences

>g568.t2 Gene=g568 Length=691
ATGTTTAACAATAATCAAGCCCGACATCCGCCTCCTCATCAAATGTATGCGCCACCACCG
CCTAGAGAAAATTATGGCAAAACTATAGGCTCAGGGCCTCAATTTTATACTAAACCACCT
ACAAATATTCCATCTAATCAAACAATTGAATTTGATGAAGGTCCGAAAATTACTGTCTTT
GTTGGTAACATTAGTGATAAGATTCCAGATGCAATGATTAAAAAATTAATAGCAGCTTGT
GGACCAGTAGCGAATTGGAAACGAGTATCAACTTTCGGTTTCTGTGAATATGATGGACCA
AAATCAGGAGCTCGAGCTGTTAGACTATTGCATGGATATGAAGTTGATGGCAAAAAATTA
GTAGCAAAAGTAGATGCCAAAAATCAAGCTTTACTTGACACAGCAAAAGATGAAGAAAAT
AAAAAGTCGGATGCAAATAACACTAGAAATTCTGATGCAGCAAATGAAAAGAAGAATGAC
GAGATTGCACTTGAACGATTGCATCAAATTGTAGAAGAATATAAAGATGAATTAAAAACA
GCAAATTCAGCTGAAAATCAACAACCGCATCCACGAAGTAAGCAAACTGTGCCATCAATT
GAAATTGAGGAAGGGAAACGAGATTTAATAAATAAAGAAATTGGAAGATTTCGTAAGATT
GCTGAAGAAGAAGAGGCCAAGAAAGAAAAAG

>g568.t2 Gene=g568 Length=230
MFNNNQARHPPPHQMYAPPPPRENYGKTIGSGPQFYTKPPTNIPSNQTIEFDEGPKITVF
VGNISDKIPDAMIKKLIAACGPVANWKRVSTFGFCEYDGPKSGARAVRLLHGYEVDGKKL
VAKVDAKNQALLDTAKDEENKKSDANNTRNSDAANEKKNDEIALERLHQIVEEYKDELKT
ANSAENQQPHPRSKQTVPSIEIEEGKRDLINKEIGRFRKIAEEEEAKKEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g568.t2 CDD cd12446 RRM_RBM25 58 132 8.52566E-33
6 g568.t2 Coils Coil Coil 121 148 -
5 g568.t2 Coils Coil Coil 157 187 -
4 g568.t2 Gene3D G3DSA:3.30.70.330 - 51 157 1.3E-12
11 g568.t2 MobiDBLite mobidb-lite consensus disorder prediction 135 161 -
9 g568.t2 MobiDBLite mobidb-lite consensus disorder prediction 180 205 -
10 g568.t2 MobiDBLite mobidb-lite consensus disorder prediction 181 195 -
2 g568.t2 PANTHER PTHR18806 RBM25 PROTEIN 8 228 9.6E-57
1 g568.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 59 120 1.8E-6
12 g568.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 57 127 10.343
8 g568.t2 SMART SM00360 rrm1_1 58 123 6.3E-9
3 g568.t2 SUPERFAMILY SSF54928 RNA-binding domain, RBD 22 123 3.12E-14

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g568/g568.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g568.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003676 nucleic acid binding MF

KEGG

Orthology

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.

Raw TPM values