Gene loci information

Transcript annotation

  • This transcript has been annotated as Polyubiquitin-C.

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.t8 TTS g4090.t8 30514378 30514378
chr_3 g4090 g4090.t8 isoform g4090.t8 30514456 30515575
chr_3 g4090 g4090.t8 exon g4090.t8.exon1 30514456 30514617
chr_3 g4090 g4090.t8 cds g4090.t8.CDS1 30514456 30514617
chr_3 g4090 g4090.t8 exon g4090.t8.exon2 30515074 30515575
chr_3 g4090 g4090.t8 cds g4090.t8.CDS2 30515074 30515532
chr_3 g4090 g4090.t8 TSS g4090.t8 30516047 30516047

Sequences

>g4090.t8 Gene=g4090 Length=664
AAAACAATCACACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAATCC
AGGACAAAGAAGGAATTCACCCAGATCAACAACGTCTTATCTTTGCTGGAAAACAATTGG
AAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATCAACATTGCATTTGGTTC
TTCGTCTTCGTGGCGTATGCAAATCTTTGTAAAGACTTTGACTGGCAAAACAATCACACT
CGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAAATCCAGGACAAAGAAGG
AATTCCACCAGATCAACAACGTCTTATCTTCGCTGGAAAACAATTGGAAGACGGCCGCAC
TTTAAGCGATTACAATATTCAAAAGGAATCAACATTGCATTTGGTTCTTCGTCTTCGTGG
CGGTATGCAAATCTTTGTAAAGACTTTGACTGGCAAAACAATCACACTCGAAGTTGAGCC
ATCAGACACAATTGAAAATGTCAAAGCAAAAATCCAGGACAAAGAAGGAATTCCACCAGA
TCAACAACGTCTTATCTTCGCTGGAAAACAATTGGAAGACGGCCGCACTTTAAGCGATTA
CAAATTCAAAAGGAATCAACATTGCATTTGGTTCTTCGTCTTCGTGGAGGAAACTAATCA
TTGA

>g4090.t8 Gene=g4090 Length=206
MSKQNPGQRRNSPRSTTSYLCWKTIGRRPHFKRLQYSKGINIAFGSSSSWRMQIFVKTLT
GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL
VLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG
RTLSDYKFKRNQHCIWFFVFVEETNH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g4090.t8 CDD cd01803 Ubl_ubiquitin 52 127 3.74192E-55
10 g4090.t8 Gene3D G3DSA:3.10.20.90 - 46 127 1.3E-46
11 g4090.t8 Gene3D G3DSA:3.10.20.90 - 128 196 2.3E-35
3 g4090.t8 PANTHER PTHR10666:SF238 GH17761P 33 190 1.5E-108
4 g4090.t8 PANTHER PTHR10666 UBIQUITIN 33 190 1.5E-108
6 g4090.t8 PRINTS PR00348 Ubiquitin signature 62 82 1.1E-38
5 g4090.t8 PRINTS PR00348 Ubiquitin signature 83 103 1.1E-38
7 g4090.t8 PRINTS PR00348 Ubiquitin signature 104 125 1.1E-38
1 g4090.t8 Pfam PF00240 Ubiquitin family 54 125 4.6E-34
2 g4090.t8 Pfam PF00240 Ubiquitin family 130 191 3.2E-27
13 g4090.t8 ProSitePatterns PS00299 Ubiquitin domain signature. 78 103 -
14 g4090.t8 ProSitePatterns PS00299 Ubiquitin domain signature. 154 179 -
17 g4090.t8 ProSiteProfiles PS50053 Ubiquitin domain profile. 52 127 31.018
18 g4090.t8 ProSiteProfiles PS50053 Ubiquitin domain profile. 128 189 24.333
16 g4090.t8 SMART SM00213 ubq_7 52 123 2.9E-36
15 g4090.t8 SMART SM00213 ubq_7 128 203 4.3E-27
8 g4090.t8 SUPERFAMILY SSF54236 Ubiquitin-like 20 127 1.1E-36
9 g4090.t8 SUPERFAMILY SSF54236 Ubiquitin-like 127 191 2.03E-27

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