Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquilin-1.

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 g3004 g3004.t3 TSS g3004.t3 21915593 21915593
chr_3 g3004 g3004.t3 isoform g3004.t3 21915821 21916990
chr_3 g3004 g3004.t3 exon g3004.t3.exon1 21915821 21915916
chr_3 g3004 g3004.t3 cds g3004.t3.CDS1 21915821 21915916
chr_3 g3004 g3004.t3 exon g3004.t3.exon2 21916198 21916329
chr_3 g3004 g3004.t3 cds g3004.t3.CDS2 21916198 21916329
chr_3 g3004 g3004.t3 exon g3004.t3.exon3 21916390 21916990
chr_3 g3004 g3004.t3 cds g3004.t3.CDS3 21916390 21916989
chr_3 g3004 g3004.t3 TTS g3004.t3 NA NA

Sequences

>g3004.t3 Gene=g3004 Length=829
ATGGCAGAAGGATCATCAAATCGTATTACGATAACAGTAAAAACACCTAAGGATAAGAAA
GATGTTGAAGTTGAAGAAGATTCTACAGTAGAGAAGTTCAAAGTTCTTGTTGCTGAAAAG
TTTGAAGCTGAAGTTGAGCAATTGTGCTTGATTTTTGCTGGAAAAATTATGAAAGATGCA
GACACTCTTAAAAGTCACAATATAAAAGACGGATTGACAGTTCATTTGGTTATCAAAGCT
CCACCAAAACCTGAAGCAGAAGGTCCAACACGACGACCAGCAGACGTACGTCAAACACCA
TTCGGTTTAAATCAAATTGGTGGTCTATCAGGACTTGAAGCGCTCGGTGCTAATTCAAGT
ACATTCATGGATATGCAATCTCGAATGCAGCATGAATTGATGGGGAATCCTGAGTTAATG
AGAACAATTTTAGATAACCCCTTAGTTCAACAAATGCTTAATAATCCAGACACAATGAGA
ACCTTAATTACGAGCAATCCTCAAATGCAAGATTTAATGCAGCGTAATCCAGAAATTTCT
CACATGCTCAATAATCCCGAATTGTTGCGACAAACTATGGAACTTGCAAGGAATCCAGCT
ATGTTGCAAGAGTTGATGCGTTCACACGATAGAGCAATGTCTAATTTGGAATCAGTTCCA
GGTGGTTATAATGCGCTACATCGCATTTATCGTGATATTCAAGAGCCAATGCTGAATGCA
GCTTCTGGAGCATTTTCATCAAACCCATTCAGTGGATTAGTTGATAATGGAGGTTCTGAG
AATCCTCAACAAGGAAGTGAAAATCGTGAACCATTACCAAATCCATGGG

>g3004.t3 Gene=g3004 Length=276
MAEGSSNRITITVKTPKDKKDVEVEEDSTVEKFKVLVAEKFEAEVEQLCLIFAGKIMKDA
DTLKSHNIKDGLTVHLVIKAPPKPEAEGPTRRPADVRQTPFGLNQIGGLSGLEALGANSS
TFMDMQSRMQHELMGNPELMRTILDNPLVQQMLNNPDTMRTLITSNPQMQDLMQRNPEIS
HMLNNPELLRQTMELARNPAMLQELMRSHDRAMSNLESVPGGYNALHRIYRDIQEPMLNA
ASGAFSSNPFSGLVDNGGSENPQQGSENREPLPNPW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3004.t3 CDD cd01808 Ubl_PLICs 7 79 3.17537E-43
10 g3004.t3 Gene3D G3DSA:3.10.20.90 - 1 86 9.5E-25
11 g3004.t3 Gene3D G3DSA:1.10.260.100 - 168 222 1.6E-7
16 g3004.t3 MobiDBLite mobidb-lite consensus disorder prediction 255 276 -
2 g3004.t3 PANTHER PTHR10677 UBIQUILIN 6 88 9.2E-102
4 g3004.t3 PANTHER PTHR10677:SF21 UBIQUILIN-4 6 88 9.2E-102
3 g3004.t3 PANTHER PTHR10677 UBIQUILIN 103 276 9.2E-102
5 g3004.t3 PANTHER PTHR10677:SF21 UBIQUILIN-4 103 276 9.2E-102
7 g3004.t3 PRINTS PR00348 Ubiquitin signature 18 38 5.9E-5
8 g3004.t3 PRINTS PR00348 Ubiquitin signature 39 59 5.9E-5
6 g3004.t3 PRINTS PR00348 Ubiquitin signature 60 81 5.9E-5
1 g3004.t3 Pfam PF00240 Ubiquitin family 11 80 3.0E-20
17 g3004.t3 ProSiteProfiles PS50053 Ubiquitin domain profile. 9 79 17.104
13 g3004.t3 SMART SM00213 ubq_7 9 79 3.1E-17
14 g3004.t3 SMART SM00727 CBM 136 165 12.0
15 g3004.t3 SMART SM00727 CBM 166 205 4.9E-8
9 g3004.t3 SUPERFAMILY SSF54236 Ubiquitin-like 4 86 4.37E-23

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