Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t2 TTS g4090.t2 30514378 30514378
chr_3 g4090 g4090.t2 isoform g4090.t2 30514456 30515372
chr_3 g4090 g4090.t2 exon g4090.t2.exon1 30514456 30514613
chr_3 g4090 g4090.t2 cds g4090.t2.CDS1 30514527 30514613
chr_3 g4090 g4090.t2 exon g4090.t2.exon2 30514849 30515372
chr_3 g4090 g4090.t2 cds g4090.t2.CDS2 30514849 30515151
chr_3 g4090 g4090.t2 TSS g4090.t2 30516047 30516047

Sequences

>g4090.t2 Gene=g4090 Length=682
TCTTTGTAAAGACTTTGACTGGCAAAACAATCACACTCGAAGTTGAGCCATCAGACACAA
TTGAAAATGTCAAAGCAAAAATCCAGGACAAAGAAGGAATTCCACCAGATCAACAACGTC
TTATCTTCGCTGGAAAACAATTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAA
AGGAATCAACATTGCATTTGGTTCTTCGTCTTCGTGGCGGTATGCAAATCTTTGTAAAGA
CTTTGACTGGCAAAACAATCACACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCA
AAGCAAAAATCCAAGACAAAGAAGGAATTCCACCAGATCAACAACGTCTTATCTTTGCTG
GAAAACAATTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATCAACAT
TGCATTTGGTTCTTCGTCTTCGTGGCGGTATGCAAATCTTTGTAAAGACTTTGACTGGCA
AAACAATCACACTCGAAGTTGAGCCATCAGACACAATTGAAAATCAAAAATCCAGGACAA
AGAAGGAATTCCACCAGATCAACAACGTCTTATCTTCGCTGGAAAACAATTGGAAGACGG
CCGCACTTTAAGCGATTACAAATTCAAAAGGAATCAACATTGCATTTGGTTCTTCGTCTT
CGTGGAGGAAACTAATCATTGA

>g4090.t2 Gene=g4090 Length=129
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENQKSRTKKEFHQINNVLSSL
ENNWKTAAL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4090.t2 CDD cd01803 Ubl_ubiquitin 1 76 1.89154E-53
12 g4090.t2 Coils Coil Coil 103 123 -
11 g4090.t2 Gene3D G3DSA:3.10.20.90 - 1 76 1.2E-46
10 g4090.t2 Gene3D G3DSA:3.10.20.90 - 77 115 2.6E-13
3 g4090.t2 PANTHER PTHR10666:SF238 GH17761P 1 106 8.7E-77
4 g4090.t2 PANTHER PTHR10666 UBIQUITIN 1 106 8.7E-77
7 g4090.t2 PRINTS PR00348 Ubiquitin signature 11 31 4.1E-39
6 g4090.t2 PRINTS PR00348 Ubiquitin signature 32 52 4.1E-39
5 g4090.t2 PRINTS PR00348 Ubiquitin signature 53 74 4.1E-39
2 g4090.t2 Pfam PF00240 Ubiquitin family 3 74 1.5E-34
1 g4090.t2 Pfam PF00240 Ubiquitin family 79 110 7.0E-6
15 g4090.t2 ProSitePatterns PS00299 Ubiquitin domain signature. 27 52 -
16 g4090.t2 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 76 31.018
14 g4090.t2 SMART SM00213 ubq_7 1 72 2.9E-36
9 g4090.t2 SUPERFAMILY SSF54236 Ubiquitin-like 1 76 2.69E-35
8 g4090.t2 SUPERFAMILY SSF54236 Ubiquitin-like 76 108 3.22E-7

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