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.t4 TTS g4090.t4 30514378 30514378
chr_3 g4090 g4090.t4 isoform g4090.t4 30514456 30515532
chr_3 g4090 g4090.t4 exon g4090.t4.exon1 30514456 30514634
chr_3 g4090 g4090.t4 cds g4090.t4.CDS1 30514527 30514634
chr_3 g4090 g4090.t4 exon g4090.t4.exon2 30514849 30515532
chr_3 g4090 g4090.t4 cds g4090.t4.CDS2 30514849 30515532
chr_3 g4090 g4090.t4 TSS g4090.t4 30516047 30516047

Sequences

>g4090.t4 Gene=g4090 Length=863
ATGTCAAAGCAAAATCCAGGACAAAGAAGGAATTCACCCAGATCAACAACGTCTTATCTT
TGCTGGAAAACAATTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATC
AACATTGCATTTGGTTCTTCGTCTTCGTGGCGTATGCAAATCTTTGTAAAGACTTTGACT
GGCAAAACAATCACACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAA
ATCCAGGACAAAGAAGGAATTCCACCAGATCAACAACGTCTTATCTTCGCTGGAAAACAA
TTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATCAACATTGCATTTG
GTTCTTCGTCTTCGTGGCGGTATGCAAATCTTTGTAAAGACTTTGACTGGCAAAACAATC
ACACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAAATCCAAGACAAA
GAAGGAATTCCACCAGATCAACAACGTCTTATCTTTGCTGGAAAACAATTGGAAGACGGC
CGCACTTTAAGCGATTACAATATTCAAAAGGAATCAACATTGCATTTGGTTCTTCGTCTT
CGTGGCGGTATGCAAATCTTTGTAAAGACTTTGACTGGCAAAACAATCACACTCGAAGTT
GAGCCATCAGACACAATTGAAAATACACAATTGAAAATGTCAAAGCAAAAATCCAGGACA
AAGAAGGAATTCCACCAGATCAACAACGTCTTATCTTCGCTGGAAAACAATTGGAAGACG
GCCGCACTTTAAGCGATTACAAATTCAAAAGGAATCAACATTGCATTTGGTTCTTCGTCT
TCGTGGAGGAAACTAATCATTGA

>g4090.t4 Gene=g4090 Length=263
MSKQNPGQRRNSPRSTTSYLCWKTIGRRPHFKRLQYSKGINIAFGSSSSWRMQIFVKTLT
GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL
VLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG
RTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENTQLKMSKQKSRT
KKEFHQINNVLSSLENNWKTAAL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g4090.t4 CDD cd01803 Ubl_ubiquitin 52 127 7.52999E-53
16 g4090.t4 CDD cd01803 Ubl_ubiquitin 128 203 7.52999E-53
15 g4090.t4 Coils Coil Coil 237 257 -
13 g4090.t4 Gene3D G3DSA:3.10.20.90 - 46 127 3.8E-46
12 g4090.t4 Gene3D G3DSA:3.10.20.90 - 128 203 4.4E-46
14 g4090.t4 Gene3D G3DSA:3.10.20.90 - 204 247 4.1E-12
4 g4090.t4 PANTHER PTHR10666:SF238 GH17761P 33 235 4.0E-143
5 g4090.t4 PANTHER PTHR10666 UBIQUITIN 33 235 4.0E-143
7 g4090.t4 PRINTS PR00348 Ubiquitin signature 62 82 1.6E-38
6 g4090.t4 PRINTS PR00348 Ubiquitin signature 83 103 1.6E-38
8 g4090.t4 PRINTS PR00348 Ubiquitin signature 104 125 1.6E-38
1 g4090.t4 Pfam PF00240 Ubiquitin family 54 125 7.4E-34
2 g4090.t4 Pfam PF00240 Ubiquitin family 130 201 7.4E-34
3 g4090.t4 Pfam PF00240 Ubiquitin family 206 237 4.1E-5
20 g4090.t4 ProSitePatterns PS00299 Ubiquitin domain signature. 78 103 -
21 g4090.t4 ProSitePatterns PS00299 Ubiquitin domain signature. 154 179 -
23 g4090.t4 ProSiteProfiles PS50053 Ubiquitin domain profile. 52 127 31.018
22 g4090.t4 ProSiteProfiles PS50053 Ubiquitin domain profile. 128 203 31.018
18 g4090.t4 SMART SM00213 ubq_7 52 123 2.9E-36
19 g4090.t4 SMART SM00213 ubq_7 128 199 2.9E-36
11 g4090.t4 SUPERFAMILY SSF54236 Ubiquitin-like 20 127 2.24E-36
10 g4090.t4 SUPERFAMILY SSF54236 Ubiquitin-like 127 203 6.43E-35
9 g4090.t4 SUPERFAMILY SSF54236 Ubiquitin-like 203 237 8.52E-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