Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g4083 g4083.t1 isoform g4083.t1 30501686 30502568
chr_3 g4083 g4083.t1 exon g4083.t1.exon1 30501686 30502223
chr_3 g4083 g4083.t1 cds g4083.t1.CDS1 30501686 30502223
chr_3 g4083 g4083.t1 exon g4083.t1.exon2 30502281 30502496
chr_3 g4083 g4083.t1 cds g4083.t1.CDS2 30502281 30502496
chr_3 g4083 g4083.t1 exon g4083.t1.exon3 30502555 30502568
chr_3 g4083 g4083.t1 cds g4083.t1.CDS3 30502555 30502568
chr_3 g4083 g4083.t1 TSS g4083.t1 30502687 30502687
chr_3 g4083 g4083.t1 TTS g4083.t1 NA NA

Sequences

>g4083.t1 Gene=g4083 Length=768
ATGGATTGTGAAGAAATTGATTTTGATAATGAGATGATGATTGATGAACAGACTGACAAT
GAAATCGTCGATGAAATAACAAATTTGGAAGCTAATGTTAATACTGATAGCGAACTGAAA
GATGATTCTTGTGAGAATAAAGTATTAACTGATGTTAACAATATTATAACAAAAGACGAT
TCCACTGTTGTAGCTGATGATAAAACTAGTCAAATGTTTAAAAATGAAACAGGTTGGGAA
TCAATGAAGATAGAAGAAAACTTGAAATGTCCAGAACTAAATGACTCAGGATATGCATCA
GACGAGAACATGAAATTGGATATTGAAATAAACGAAAAAGAAAGTATACCTTTGTGTATG
AATAAAAAAGAAACAGTTTATGAAGCTCTGATGAAAGCATCGTCTATAAGACAGATTGAA
TACGAAGAATATGATTTGTTTTATAATGGAAAAGCTTTATCTCTCAGTGTTGCTCTTGGT
GATGTAGGTTTGACACAAAACAGTCGCTTGCGATTGGTTCAACGACCATATCCTGTTTTC
GTTCGTATTGGAGGACGTAGTGAAACTTATGAGGTTCGTTCTTCTGACACAGTCGGACAA
TTGAAGGAAAAAATAAGTGACAACAAGGCAATACCTGCATTTTCTCAACGTTTGTTGTAT
GAAAGTCGAGAATTAGACAATTCTTGGACTATAGAATATTCCAAAATTCGCAAAAATGCA
ATATTGGATCTTGCTCAACGCTTATATGGAGGCGGACATTCATCTTAA

>g4083.t1 Gene=g4083 Length=255
MDCEEIDFDNEMMIDEQTDNEIVDEITNLEANVNTDSELKDDSCENKVLTDVNNIITKDD
STVVADDKTSQMFKNETGWESMKIEENLKCPELNDSGYASDENMKLDIEINEKESIPLCM
NKKETVYEALMKASSIRQIEYEEYDLFYNGKALSLSVALGDVGLTQNSRLRLVQRPYPVF
VRIGGRSETYEVRSSDTVGQLKEKISDNKAIPAFSQRLLYESRELDNSWTIEYSKIRKNA
ILDLAQRLYGGGHSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4083.t1 CDD cd17039 Ubl_ubiquitin_like 108 173 0.0009648
12 g4083.t1 CDD cd17039 Ubl_ubiquitin_like 179 244 0.0000000
10 g4083.t1 Gene3D G3DSA:3.10.20.90 - 97 177 0.0000024
11 g4083.t1 Gene3D G3DSA:3.10.20.90 - 178 251 0.0000000
3 g4083.t1 PANTHER PTHR10666 UBIQUITIN 180 252 0.0000000
4 g4083.t1 PANTHER PTHR10666:SF288 POLYUBIQUITIN 10 180 252 0.0000000
7 g4083.t1 PRINTS PR00348 Ubiquitin signature 186 206 0.0000003
6 g4083.t1 PRINTS PR00348 Ubiquitin signature 207 227 0.0000003
5 g4083.t1 PRINTS PR00348 Ubiquitin signature 228 249 0.0000003
2 g4083.t1 Pfam PF00240 Ubiquitin family 112 176 0.0000160
1 g4083.t1 Pfam PF00240 Ubiquitin family 179 247 0.0000000
17 g4083.t1 ProSiteProfiles PS50053 Ubiquitin domain profile. 104 175 10.4620000
16 g4083.t1 ProSiteProfiles PS50053 Ubiquitin domain profile. 177 251 16.7340000
15 g4083.t1 SMART SM00213 ubq_7 104 175 14.0000000
14 g4083.t1 SMART SM00213 ubq_7 177 247 0.0000000
9 g4083.t1 SUPERFAMILY SSF54236 Ubiquitin-like 97 175 0.0000007
8 g4083.t1 SUPERFAMILY SSF54236 Ubiquitin-like 176 252 0.0000000

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:0005515 protein 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