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.t2 TTS g7142.t2 21478218 21478218
chr_2 g7142 g7142.t2 isoform g7142.t2 21478421 21479483
chr_2 g7142 g7142.t2 exon g7142.t2.exon1 21478421 21479125
chr_2 g7142 g7142.t2 cds g7142.t2.CDS1 21478421 21479125
chr_2 g7142 g7142.t2 exon g7142.t2.exon2 21479432 21479483
chr_2 g7142 g7142.t2 TSS g7142.t2 21480158 21480158

Sequences

>g7142.t2 Gene=g7142 Length=757
GAATAGGAAGCGCTTGTGTAGTGTTTTTGTTATTTGCACTCATCAGTGCTTGATGTCAAC
AACATCAGATTTATCCGTCAATGAAACATTGCCTGATTCGACAGCCTCAATAGAGGAAGA
ACATGCTTCTACAAGTGAAATTGATCAAACTCATCGATCTTCAACACAATATTCATTTAC
TCCAACAGCTGAAAATAGCAAGACTTCTACAAAACCGGATGCTGCAAAAAAGGATGATGA
AGATGACGAAGACAAACGGGATGACTCAATGTTTGTGTGTAATATTTGTTTAGATATTGC
AAAAGATTCTGTAATTACTTTTTGTGGCCATTTATATTGTTGGCCTTGCATCAACTGTTG
GCTTGAAACAAAAAGACCACAATTATGCCCGGTTTGTAAAGCAGCAATTAGTAGAAACCA
AGTGATTCCATTGTATGGGCGAAATAGTAATAGTCAACAGGATCCTCGATCAAAAAAGAT
CCCACCTCGTCCACAAGGACAAAGAACAGAACCTGATAATAATCAAGGTTTTCAAGGATT
TCAAAATTTCGGAGATGGTGGTTTTCATTTATCATTTGGAATTGGTGCTTTTCCATTTGG
ATTTTTTGCATCTAGCTTTAATAGTTTCAATTTTAATGATATTAGACCACGAAATGGTCA
GCAACCTGGTTCTCCGCAATATGAAGAAGATCAATTTTTGTCGAAAGTTTTTCTTTGGGT
GGCAATGATTTTCTTTTGTTGGCTTATTCTTGCCTAA

>g7142.t2 Gene=g7142 Length=234
MSTTSDLSVNETLPDSTASIEEEHASTSEIDQTHRSSTQYSFTPTAENSKTSTKPDAAKK
DDEDDEDKRDDSMFVCNICLDIAKDSVITFCGHLYCWPCINCWLETKRPQLCPVCKAAIS
RNQVIPLYGRNSNSQQDPRSKKIPPRPQGQRTEPDNNQGFQGFQNFGDGGFHLSFGIGAF
PFGFFASSFNSFNFNDIRPRNGQQPGSPQYEEDQFLSKVFLWVAMIFFCWLILA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g7142.t2 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 56 129 4.2E-17
16 g7142.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 67 -
18 g7142.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 21 -
15 g7142.t2 MobiDBLite mobidb-lite consensus disorder prediction 31 52 -
20 g7142.t2 MobiDBLite mobidb-lite consensus disorder prediction 53 67 -
17 g7142.t2 MobiDBLite mobidb-lite consensus disorder prediction 127 141 -
19 g7142.t2 MobiDBLite mobidb-lite consensus disorder prediction 127 154 -
2 g7142.t2 PANTHER PTHR12313:SF13 E3 UBIQUITIN-PROTEIN LIGASE RNF185 44 234 1.4E-70
3 g7142.t2 PANTHER PTHR12313 E3 UBIQUITIN-PROTEIN LIGASE RNF5-RELATED 44 234 1.4E-70
1 g7142.t2 Pfam PF00097 Zinc finger, C3HC4 type (RING finger) 76 115 1.0E-7
7 g7142.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 170 -
9 g7142.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 194 -
6 g7142.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 195 214 -
10 g7142.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 215 233 -
8 g7142.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 234 234 -
13 g7142.t2 ProSitePatterns PS00518 Zinc finger RING-type signature. 91 100 -
21 g7142.t2 ProSiteProfiles PS50089 Zinc finger RING-type profile. 76 116 12.489
14 g7142.t2 SMART SM00184 ring_2 76 115 4.1E-6
4 g7142.t2 SUPERFAMILY SSF57850 RING/U-box 71 128 2.7E-16
11 g7142.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 172 194 -
12 g7142.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 215 233 -

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.

Raw TPM values