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.t5 TTS g4090.t5 30514378 30514378
chr_3 g4090 g4090.t5 isoform g4090.t5 30514456 30515532
chr_3 g4090 g4090.t5 exon g4090.t5.exon1 30514456 30514681
chr_3 g4090 g4090.t5 cds g4090.t5.CDS1 30514643 30514681
chr_3 g4090 g4090.t5 exon g4090.t5.exon2 30515140 30515532
chr_3 g4090 g4090.t5 cds g4090.t5.CDS2 30515140 30515532
chr_3 g4090 g4090.t5 TSS g4090.t5 30516047 30516047

Sequences

>g4090.t5 Gene=g4090 Length=619
ATGTCAAAGCAAAATCCAGGACAAAGAAGGAATTCACCCAGATCAACAACGTCTTATCTT
TGCTGGAAAACAATTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATC
AACATTGCATTTGGTTCTTCGTCTTCGTGGCGTATGCAAATCTTTGTAAAGACTTTGACT
GGCAAAACAATCACACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAA
ATCCAGGACAAAGAAGGAATTCCACCAGATCAACAACGTCTTATCTTCGCTGGAAAACAA
TTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATCAACATTGCATTTG
GTTCTTCGTCTTCGTGGCGGTATGCAAATCTTTAAAGACTTTGACTGGCAAAACAATCAC
ACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAAATCCAGGACAAAGA
AGGAATTCCACCAGATCAACAACGTCTTATCTTCGCTGGAAAACAATTGGAAGACGGCCG
CACTTTAAGCGATTACAAATTCAAAAGGAATCAACATTGCATTTGGTTCTTCGTCTTCGT
GGAGGAAACTAATCATTGA

>g4090.t5 Gene=g4090 Length=143
MSKQNPGQRRNSPRSTTSYLCWKTIGRRPHFKRLQYSKGINIAFGSSSSWRMQIFVKTLT
GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL
VLRLRGGMQIFKDFDWQNNHTRS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4090.t5 CDD cd01803 Ubl_ubiquitin 52 127 5.10422E-57
8 g4090.t5 Gene3D G3DSA:3.10.20.90 - 46 141 2.3E-47
2 g4090.t5 PANTHER PTHR10666:SF238 GH17761P 52 131 3.4E-60
3 g4090.t5 PANTHER PTHR10666 UBIQUITIN 52 131 3.4E-60
5 g4090.t5 PRINTS PR00348 Ubiquitin signature 62 82 4.4E-39
4 g4090.t5 PRINTS PR00348 Ubiquitin signature 83 103 4.4E-39
6 g4090.t5 PRINTS PR00348 Ubiquitin signature 104 125 4.4E-39
1 g4090.t5 Pfam PF00240 Ubiquitin family 54 125 2.0E-34
10 g4090.t5 ProSitePatterns PS00299 Ubiquitin domain signature. 78 103 -
12 g4090.t5 ProSiteProfiles PS50053 Ubiquitin domain profile. 52 127 31.018
11 g4090.t5 SMART SM00213 ubq_7 52 123 2.9E-36
7 g4090.t5 SUPERFAMILY SSF54236 Ubiquitin-like 19 127 3.19E-37

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