Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Heterogeneous nuclear ribonucleoprotein 27C.

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_2 g5178 g5178.t5 isoform g5178.t5 7551462 7552446
chr_2 g5178 g5178.t5 exon g5178.t5.exon1 7551462 7552446
chr_2 g5178 g5178.t5 cds g5178.t5.CDS1 7551464 7552108
chr_2 g5178 g5178.t5 TSS g5178.t5 7552986 7552986
chr_2 g5178 g5178.t5 TTS g5178.t5 NA NA

Sequences

>g5178.t5 Gene=g5178 Length=985
CTTTGTGACTTTTGCTGATCCAAACAATGTGCAGGTATGTTTTTATTGCTGCTGTTATAT
TTTGTTTTTTATGTATATAAACAAAAAAAATTTTTTTACTTATTACAGGTCGTTTTGCAA
TCAGGTCCTCATAATTTGGATGGAAGGTACTTATAATTGACATATATGCATCAAATAATC
ATAACAAAAATGAAATCTCGCTAAAATGAAGCAGATTTTTCTCAACCATATGGTGTTTCA
CCTCATTCACTAACATATGGATTCTTCTTTTTATACTTTTTCTTTCTTTTTTTTTTACAT
AAAGAACCATTGACCCAAAACAATGTAATCCAAGAACTATGCAGAAACCCAAGACACGCG
GTGGCTCGTTTCCAAAAGTGTTTCTTGGTGGTCTACCATCGAATGTCACGGAAACCGATT
TACGAATGTATTTTGGGCGTTATGGGAAAGTCATGGAAGTTGTCATCATGTATGATCAAG
AGAAGAAAAAGTCTCGTGGCTTTGGTTTCTTGTCATTTGAGGATGATGCATCAGTTGAAC
GTGTTTGTACTGAGCATTACATTACATTGAATGGAAAGCAGGTCGAGATAAAGAAAGCTG
AGCCGAGAGATGGTTCGACAAATCATAAAATGAGTCAGGATGCAATTCAATCGATGGGCT
CAAATTCGAGTTGGGGTCCTCCTGGTGGACAAATGCCAAGCAGTGGAGTTAATCCAATGA
TGCAAGGTCCAAATGGGCAAATGAATGCTCCTCAACACATGAATATGATGGCTCCAAATA
TGCTTGGTGGTTATCCATCAAGTTGGAATTCACAACAACAGAGCTATGGCTATAGTGGTG
CACCAAATCATGCGGGTGCATATAATCAACAAAATTGGGGACCTGCACAAGCTCCTCAAG
CGGGTCCACCACCGCCAGCAATGGGACAATGGGGAAATTATAATGCTGCCACACCACAAA
CACAAGGCTACAATTCATCTTATGG

>g5178.t5 Gene=g5178 Length=215
MQKPKTRGGSFPKVFLGGLPSNVTETDLRMYFGRYGKVMEVVIMYDQEKKKSRGFGFLSF
EDDASVERVCTEHYITLNGKQVEIKKAEPRDGSTNHKMSQDAIQSMGSNSSWGPPGGQMP
SSGVNPMMQGPNGQMNAPQHMNMMAPNMLGGYPSSWNSQQQSYGYSGAPNHAGAYNQQNW
GPAQAPQAGPPPPAMGQWGNYNAATPQTQGYNSSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5178.t5 CDD cd12327 RRM2_DAZAP1 12 89 8.33721E-48
5 g5178.t5 Gene3D G3DSA:3.30.70.330 - 12 91 1.3E-23
9 g5178.t5 MobiDBLite mobidb-lite consensus disorder prediction 86 116 -
8 g5178.t5 MobiDBLite mobidb-lite consensus disorder prediction 96 116 -
11 g5178.t5 MobiDBLite mobidb-lite consensus disorder prediction 177 215 -
10 g5178.t5 MobiDBLite mobidb-lite consensus disorder prediction 200 215 -
2 g5178.t5 PANTHER PTHR48027:SF12 DAZ-ASSOCIATED PROTEIN 1 12 210 2.8E-49
3 g5178.t5 PANTHER PTHR48027 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN 87F-RELATED 12 210 2.8E-49
1 g5178.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 14 81 1.2E-15
12 g5178.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 12 89 17.575
7 g5178.t5 SMART SM00360 rrm1_1 13 85 1.3E-22
4 g5178.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 12 116 2.55E-23

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5178/g5178.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5178.t5.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
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