Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative E3 ubiquitin-protein ligase RNF185.

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 g7142 g7142.t5 TTS g7142.t5 21478218 21478218
chr_2 g7142 g7142.t5 isoform g7142.t5 21478421 21480095
chr_2 g7142 g7142.t5 exon g7142.t5.exon1 21478421 21478926
chr_2 g7142 g7142.t5 cds g7142.t5.CDS1 21478421 21478926
chr_2 g7142 g7142.t5 exon g7142.t5.exon2 21479044 21479125
chr_2 g7142 g7142.t5 cds g7142.t5.CDS2 21479044 21479125
chr_2 g7142 g7142.t5 exon g7142.t5.exon3 21480077 21480095
chr_2 g7142 g7142.t5 TSS g7142.t5 21480158 21480158

Sequences

>g7142.t5 Gene=g7142 Length=607
ACTATACAAATAAATAAATATGTCAACAACATCAGATTTATCCGTCAATGAAACATTGCC
TGATTCGACAGCCTCAATAGAGGAAGAACATGCTTCTACAAACAAACGGGATGACTCAAT
GTTTGTGTGTAATATTTGTTTAGATATTGCAAAAGATTCTGTAATTACTTTTTGTGGCCA
TTTATATTGTTGGCCTTGCATCAACTGTTGGCTTGAAACAAAAAGACCACAATTATGCCC
GGTTTGTAAAGCAGCAATTAGTAGAAACCAAGTGATTCCATTGTATGGGCGAAATAGTAA
TAGTCAACAGGATCCTCGATCAAAAAAGATCCCACCTCGTCCACAAGGACAAAGAACAGA
ACCTGATAATAATCAAGGTTTTCAAGGATTTCAAAATTTCGGAGATGGTGGTTTTCATTT
ATCATTTGGAATTGGTGCTTTTCCATTTGGATTTTTTGCATCTAGCTTTAATAGTTTCAA
TTTTAATGATATTAGACCACGAAATGGTCAGCAACCTGGTTCTCCGCAATATGAAGAAGA
TCAATTTTTGTCGAAAGTTTTTCTTTGGGTGGCAATGATTTTCTTTTGTTGGCTTATTCT
TGCCTAA

>g7142.t5 Gene=g7142 Length=195
MSTTSDLSVNETLPDSTASIEEEHASTNKRDDSMFVCNICLDIAKDSVITFCGHLYCWPC
INCWLETKRPQLCPVCKAAISRNQVIPLYGRNSNSQQDPRSKKIPPRPQGQRTEPDNNQG
FQGFQNFGDGGFHLSFGIGAFPFGFFASSFNSFNFNDIRPRNGQQPGSPQYEEDQFLSKV
FLWVAMIFFCWLILA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g7142.t5 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 5 114 4.6E-17
16 g7142.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 21 -
17 g7142.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 25 -
15 g7142.t5 MobiDBLite mobidb-lite consensus disorder prediction 89 115 -
2 g7142.t5 PANTHER PTHR12313:SF13 E3 UBIQUITIN-PROTEIN LIGASE RNF185 16 195 5.6E-70
3 g7142.t5 PANTHER PTHR12313 E3 UBIQUITIN-PROTEIN LIGASE RNF5-RELATED 16 195 5.6E-70
1 g7142.t5 Pfam PF00097 Zinc finger, C3HC4 type (RING finger) 37 76 7.6E-8
8 g7142.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 133 -
10 g7142.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 134 155 -
6 g7142.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 156 175 -
9 g7142.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 176 194 -
7 g7142.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 195 195 -
13 g7142.t5 ProSitePatterns PS00518 Zinc finger RING-type signature. 52 61 -
18 g7142.t5 ProSiteProfiles PS50089 Zinc finger RING-type profile. 37 77 12.489
14 g7142.t5 SMART SM00184 ring_2 37 76 4.1E-6
4 g7142.t5 SUPERFAMILY SSF57850 RING/U-box 32 89 1.59E-16
12 g7142.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 133 155 -
11 g7142.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 176 194 -

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

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. There were no conditions that were differentially expressed