Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t1 TTS g5178.t1 7550278 7550278
chr_2 g5178 g5178.t1 isoform g5178.t1 7550613 7552876
chr_2 g5178 g5178.t1 exon g5178.t1.exon1 7550613 7550749
chr_2 g5178 g5178.t1 cds g5178.t1.CDS1 7550613 7550749
chr_2 g5178 g5178.t1 exon g5178.t1.exon2 7551072 7551179
chr_2 g5178 g5178.t1 cds g5178.t1.CDS2 7551072 7551179
chr_2 g5178 g5178.t1 exon g5178.t1.exon3 7551285 7551392
chr_2 g5178 g5178.t1 cds g5178.t1.CDS3 7551285 7551392
chr_2 g5178 g5178.t1 exon g5178.t1.exon4 7551463 7552142
chr_2 g5178 g5178.t1 cds g5178.t1.CDS4 7551463 7552142
chr_2 g5178 g5178.t1 exon g5178.t1.exon5 7552301 7552338
chr_2 g5178 g5178.t1 cds g5178.t1.CDS5 7552301 7552338
chr_2 g5178 g5178.t1 exon g5178.t1.exon6 7552413 7552446
chr_2 g5178 g5178.t1 cds g5178.t1.CDS6 7552413 7552446
chr_2 g5178 g5178.t1 exon g5178.t1.exon7 7552529 7552660
chr_2 g5178 g5178.t1 cds g5178.t1.CDS7 7552529 7552660
chr_2 g5178 g5178.t1 exon g5178.t1.exon8 7552833 7552876
chr_2 g5178 g5178.t1 cds g5178.t1.CDS8 7552833 7552876
chr_2 g5178 g5178.t1 TSS g5178.t1 7552986 7552986

Sequences

>g5178.t1 Gene=g5178 Length=1281
ATGCGTATGAATGCCGGTGTCGATGTGGAGGATGATGAAAAGGGGAAGCTTTTTGTCGGT
GGCTTGAGCTGGGAAACGACACAGGATTCATTGCAACGCTATTTCAGCCGATATGGCGAA
GTTATCGATTGTGTGGTGATGAAAAATAATGAAACGGGAAGATCTAGAGGCTTTGGCTTT
GTGACTTTTGCTGATCCAAACAATGTGCAGGTCGTTTTGCAATCAGGTCCTCATAATTTG
GATGGAAGAACCATTGACCCAAAACAATGTAATCCAAGAACTATGCAGAAACCCAAGACA
CGCGGTGGCTCGTTTCCAAAAGTGTTTCTTGGTGGTCTACCATCGAATGTCACGGAAACC
GATTTACGAATGTATTTTGGGCGTTATGGGAAAGTCATGGAAGTTGTCATCATGTATGAT
CAAGAGAAGAAAAAGTCTCGTGGCTTTGGTTTCTTGTCATTTGAGGATGATGCATCAGTT
GAACGTGTTTGTACTGAGCATTACATTACATTGAATGGAAAGCAGGTCGAGATAAAGAAA
GCTGAGCCGAGAGATGGTTCGACAAATCATAAAATGAGTCAGGATGCAATTCAATCGATG
GGCTCAAATTCGAGTTGGGGTCCTCCTGGTGGACAAATGCCAAGCAGTGGAGTTAATCCA
ATGATGCAAGGTCCAAATGGGCAAATGAATGCTCCTCAACACATGAATATGATGGCTCCA
AATATGCTTGGTGGTTATCCATCAAGTTGGAATTCACAACAACAGAGCTATGGCTATAGT
GGTGCACCAAATCATGCGGGTGCATATAATCAACAAAATTGGGGACCTGCACAAGCTCCT
CAAGCGGGTCCACCACCGCCAGCAATGGGACAATGGGGAAATTATAATGCTGCCACACCA
CAAACACAAGGCTACAATTCATCTTATGACATGTATAACTCATCGACTGGTCCATCTGCA
GGATCTGGAGGCAATTGGAATTCATGGGGACCGCTAACTAATTCCGGCGCAACTAATGCC
GGATCTAGTGAGTATTATGACATGTATAATCGTCAATCAAGCACGGCAGGACCTAATATG
GGTCCACCACCGACCGCAACTGCTAATAATAAACCTCCATCAGATTATTCGTACGGGAAT
TATGGCAATTATACAAATGACCAACAACAATCGTATGGCGGTCCACGATCAGCATACGGA
AATGATTTAAATCAATATCCACCGGGTTCAGGTGATGATTACAAACGATATCTTAACCAG
AATATTAAGCAAATTATCTAA

>g5178.t1 Gene=g5178 Length=426
MRMNAGVDVEDDEKGKLFVGGLSWETTQDSLQRYFSRYGEVIDCVVMKNNETGRSRGFGF
VTFADPNNVQVVLQSGPHNLDGRTIDPKQCNPRTMQKPKTRGGSFPKVFLGGLPSNVTET
DLRMYFGRYGKVMEVVIMYDQEKKKSRGFGFLSFEDDASVERVCTEHYITLNGKQVEIKK
AEPRDGSTNHKMSQDAIQSMGSNSSWGPPGGQMPSSGVNPMMQGPNGQMNAPQHMNMMAP
NMLGGYPSSWNSQQQSYGYSGAPNHAGAYNQQNWGPAQAPQAGPPPPAMGQWGNYNAATP
QTQGYNSSYDMYNSSTGPSAGSGGNWNSWGPLTNSGATNAGSSEYYDMYNRQSSTAGPNM
GPPPTATANNKPPSDYSYGNYGNYTNDQQQSYGGPRSAYGNDLNQYPPGSGDDYKRYLNQ
NIKQII

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5178.t1 CDD cd12574 RRM1_DAZAP1 16 97 3.76371E-55
10 g5178.t1 CDD cd12327 RRM2_DAZAP1 106 183 2.42765E-45
8 g5178.t1 Gene3D G3DSA:3.30.70.330 - 15 87 1.8E-25
7 g5178.t1 Gene3D G3DSA:3.30.70.330 - 106 185 4.6E-23
14 g5178.t1 MobiDBLite mobidb-lite consensus disorder prediction 180 210 -
13 g5178.t1 MobiDBLite mobidb-lite consensus disorder prediction 190 210 -
3 g5178.t1 PANTHER PTHR48027:SF12 DAZ-ASSOCIATED PROTEIN 1 8 402 3.3E-102
4 g5178.t1 PANTHER PTHR48027 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN 87F-RELATED 8 402 3.3E-102
2 g5178.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 17 85 1.6E-16
1 g5178.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 108 175 3.9E-15
16 g5178.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 15 102 17.83
15 g5178.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 106 183 17.575
12 g5178.t1 SMART SM00360 rrm1_1 16 88 1.0E-24
11 g5178.t1 SMART SM00360 rrm1_1 107 179 1.3E-22
5 g5178.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 13 100 9.94E-26
6 g5178.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 106 210 1.18E-22

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5178/g5178.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5178.t1.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

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