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.t3 TTS g4090.t3 30514378 30514378
chr_3 g4090 g4090.t3 isoform g4090.t3 30514456 30515532
chr_3 g4090 g4090.t3 exon g4090.t3.exon1 30514456 30514476
chr_3 g4090 g4090.t3 cds g4090.t3.CDS1 30514463 30514476
chr_3 g4090 g4090.t3 exon g4090.t3.exon2 30514704 30515532
chr_3 g4090 g4090.t3 cds g4090.t3.CDS2 30514704 30515532
chr_3 g4090 g4090.t3 TSS g4090.t3 30516047 30516047

Sequences

>g4090.t3 Gene=g4090 Length=850
ATGTCAAAGCAAAATCCAGGACAAAGAAGGAATTCACCCAGATCAACAACGTCTTATCTT
TGCTGGAAAACAATTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATC
AACATTGCATTTGGTTCTTCGTCTTCGTGGCGTATGCAAATCTTTGTAAAGACTTTGACT
GGCAAAACAATCACACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAA
ATCCAGGACAAAGAAGGAATTCCACCAGATCAACAACGTCTTATCTTCGCTGGAAAACAA
TTGGAAGACGGCCGCACTTTAAGCGATTACAATATTCAAAAGGAATCAACATTGCATTTG
GTTCTTCGTCTTCGTGGCGGTATGCAAATCTTTGTAAAGACTTTGACTGGCAAAACAATC
ACACTCGAAGTTGAGCCATCAGACACAATTGAAAATGTCAAAGCAAAAATCCAAGACAAA
GAAGGAATTCCACCAGATCAACAACGTCTTATCTTTGCTGGAAAACAATTGGAAGACGGC
CGCACTTTAAGCGATTACAATATTCAAAAGGAATCAACATTGCATTTGGTTCTTCGTCTT
CGTGGCGGTATGCAAATCTTTGTAAAGACTTTGACTGGCAAAACAATCACACTCGAAGTT
GAGCCATCAGACACAATTGAAAATGTCAAAGCAAAAATCCAGGACAAAGAAGGAATTCCA
CCAGATCAACAACGTCTTATCTTTGCTGGAAAACAATTGGAAGACGGCCGCACTTTAAGC
GATTACAATATTCAAAAGGAATCAACATTGCATTTGGTTCTTCGTCTTCGTGGAGGAAAC
TAATCATTGA

>g4090.t3 Gene=g4090 Length=280
MSKQNPGQRRNSPRSTTSYLCWKTIGRRPHFKRLQYSKGINIAFGSSSSWRMQIFVKTLT
GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL
VLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG
RTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIP
PDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g4090.t3 CDD cd01803 Ubl_ubiquitin 52 127 4.17725E-52
18 g4090.t3 CDD cd01803 Ubl_ubiquitin 128 203 4.17725E-52
17 g4090.t3 CDD cd01803 Ubl_ubiquitin 204 279 4.17725E-52
15 g4090.t3 Gene3D G3DSA:3.10.20.90 - 46 127 4.2E-46
14 g4090.t3 Gene3D G3DSA:3.10.20.90 - 128 203 5.0E-46
16 g4090.t3 Gene3D G3DSA:3.10.20.90 - 204 280 5.3E-46
4 g4090.t3 PANTHER PTHR10666 UBIQUITIN 52 206 2.7E-230
6 g4090.t3 PANTHER PTHR10666:SF357 - 52 206 2.7E-230
5 g4090.t3 PANTHER PTHR10666 UBIQUITIN 121 279 2.7E-230
7 g4090.t3 PANTHER PTHR10666:SF357 - 121 279 2.7E-230
9 g4090.t3 PRINTS PR00348 Ubiquitin signature 62 82 2.5E-38
8 g4090.t3 PRINTS PR00348 Ubiquitin signature 83 103 2.5E-38
10 g4090.t3 PRINTS PR00348 Ubiquitin signature 104 125 2.5E-38
1 g4090.t3 Pfam PF00240 Ubiquitin family 54 125 8.4E-34
2 g4090.t3 Pfam PF00240 Ubiquitin family 130 201 8.4E-34
3 g4090.t3 Pfam PF00240 Ubiquitin family 206 277 8.4E-34
21 g4090.t3 ProSitePatterns PS00299 Ubiquitin domain signature. 78 103 -
22 g4090.t3 ProSitePatterns PS00299 Ubiquitin domain signature. 154 179 -
20 g4090.t3 ProSitePatterns PS00299 Ubiquitin domain signature. 230 255 -
28 g4090.t3 ProSiteProfiles PS50053 Ubiquitin domain profile. 52 127 31.018
27 g4090.t3 ProSiteProfiles PS50053 Ubiquitin domain profile. 128 203 31.018
26 g4090.t3 ProSiteProfiles PS50053 Ubiquitin domain profile. 204 279 31.018
23 g4090.t3 SMART SM00213 ubq_7 52 123 2.9E-36
25 g4090.t3 SMART SM00213 ubq_7 128 199 2.9E-36
24 g4090.t3 SMART SM00213 ubq_7 204 275 2.9E-36
11 g4090.t3 SUPERFAMILY SSF54236 Ubiquitin-like 20 127 2.64E-36
12 g4090.t3 SUPERFAMILY SSF54236 Ubiquitin-like 126 203 3.94E-35
13 g4090.t3 SUPERFAMILY SSF54236 Ubiquitin-like 203 279 4.56E-35

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

Pathway

  • This transcript belongs to the following pathways

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