Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Polyubiquitin .

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 g4090 g4090.t7 TTS g4090.t7 30514378 30514378
chr_3 g4090 g4090.t7 isoform g4090.t7 30514456 30515532
chr_3 g4090 g4090.t7 exon g4090.t7.exon1 30514456 30514657
chr_3 g4090 g4090.t7 cds g4090.t7.CDS1 30514456 30514657
chr_3 g4090 g4090.t7 exon g4090.t7.exon2 30515342 30515532
chr_3 g4090 g4090.t7 cds g4090.t7.CDS2 30515342 30515532
chr_3 g4090 g4090.t7 TSS g4090.t7 30516047 30516047

Sequences

>g4090.t7 Gene=g4090 Length=393
ATGTCAAAGCAAAATCCAGGACAAAGAAGGAATTCACCCAGATCAACAACGTCTTATCTT
TGCTGGAAAACAATTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATC
AACATTGCATTTGGTTCTTCGTCTTCGTGGCGTATGCAAATCTTTGTAAAGACTTTGACT
GGCAAAACAATCACACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAA
ATCCAGGACAAAGAAGGAATTCCACCAGATCAACAACGTCTTATCTTCGCTGGAAAACAA
TTGGAAGACGGCCGCACTTTAAGCGATTACAAATTCAAAAGGAATCAACATTGCATTTGG
TTCTTCGTCTTCGTGGAGGAAACTAATCATTGA

>g4090.t7 Gene=g4090 Length=130
MSKQNPGQRRNSPRSTTSYLCWKTIGRRPHFKRLQYSKGINIAFGSSSSWRMQIFVKTLT
GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYKFKRNQHCIW
FFVFVEETNH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4090.t7 Gene3D G3DSA:3.10.20.90 - 46 128 7.9E-36
2 g4090.t7 PANTHER PTHR10666:SF238 GH17761P 52 114 8.3E-42
3 g4090.t7 PANTHER PTHR10666 UBIQUITIN 52 114 8.3E-42
5 g4090.t7 PRINTS PR00348 Ubiquitin signature 62 82 1.3E-25
4 g4090.t7 PRINTS PR00348 Ubiquitin signature 83 103 1.3E-25
6 g4090.t7 PRINTS PR00348 Ubiquitin signature 104 125 1.3E-25
1 g4090.t7 Pfam PF00240 Ubiquitin family 54 115 1.1E-27
9 g4090.t7 ProSitePatterns PS00299 Ubiquitin domain signature. 78 103 -
11 g4090.t7 ProSiteProfiles PS50053 Ubiquitin domain profile. 52 113 24.333
10 g4090.t7 SMART SM00213 ubq_7 52 127 4.3E-27
7 g4090.t7 SUPERFAMILY SSF54236 Ubiquitin-like 19 115 1.81E-29

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. There were no conditions that were differentially expressed