General information for g3004.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquilin-1.
Parent gene
- The parent gene g3004 is located on chr_3: 21916990..21918435 (+ strand)
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.t10 | TSS | g3004.t10 | 21915593 | 21915593 |
| chr_3 | g3004 | g3004.t10 | isoform | g3004.t10 | 21916390 | 21918043 |
| chr_3 | g3004 | g3004.t10 | exon | g3004.t10.exon1 | 21916390 | 21917581 |
| chr_3 | g3004 | g3004.t10 | cds | g3004.t10.CDS1 | 21916528 | 21917581 |
| chr_3 | g3004 | g3004.t10 | exon | g3004.t10.exon2 | 21917663 | 21918043 |
| chr_3 | g3004 | g3004.t10 | cds | g3004.t10.CDS2 | 21917663 | 21917739 |
| chr_3 | g3004 | g3004.t10 | TTS | g3004.t10 | 21918308 | 21918308 |
Sequences
>g3004.t10 Gene=g3004 Length=1573
GTTATCAAAGCTCCACCAAAACCTGAAGCAGAAGGTCCAACACGACGACCAGCAGACGTA
CGTCAAACACCATTCGGTTTAAATCAAATTGGTGGTCTATCAGGACTTGAAGCGCTCGGT
GCTAATTCAAGTACATTCATGGATATGCAATCTCGAATGCAGCATGAATTGATGGGGAAT
CCTGAGTTAATGAGAACAATTTTAGATAACCCCTTAGTTCAACAAATGCTTAATAATCCA
GACACAATGAGAACCTTAATTACGAGCAATCCTCAAATGCAAGATTTAATGCAGCGTAAT
CCAGAAATTTCTCACATGCTCAATAATCCCGAATTGTTGCGACAAACTATGGAACTTGCA
AGGAATCCAGCTATGTTGCAAGAGTTGATGCGTTCACACGATAGAGCAATGTCTAATTTG
GAATCAGTTCCAGGTGGTTATAATGCGCTACATCGCATTTATCGTGATATTCAAGAGCCA
ATGCTGAATGCAGCTTCTGGAGCATTTTCATCAAACCCATTCAGTGGATTAGTTGATAAT
GGAGGTTCTGAGAATCCTCAACAAGGAAGTGAAAATCGTGAACCATTACCAAATCCATGG
GGCGGTAGTGGAAATCAAAATTCCCGACCAGCTCCACCACCAAATAATATTTTAAACACT
CCAGCAATGCAAAGTCTTTTACAACAAATGGGAGAAAATCCTGAAATGATGTCAACTATG
ATGAATGCACCATATATGCGTTCAATGATGGAAGCACTTTCACAAGATCCGAATATGGCG
GCAAATTTGATTAGTCAAAGTCCTCTTCTTCAAGCAAATCCACAATTGCAAGATCAAATG
AGAACAATGATGCCGCAACTTTTACAGCAAATGCAAAATCCAGAAGTTCAAAATATGCTG
TCCAATCCTGATGCATTGAATGCAATCTTACAAATTCAACAAGGCATGGAACAACTTCGA
CAAGCGGCACCAGGATTAGTTGGAACCATGGGAATTCCACCACCTCCTCCCGGAACGAAT
CAGCCACCACAAACTGGAAACACACCGAATGCACCAAATCAACAACTTTTTAATGACTTT
ATGCAACGAATGCTTAATGGAATGACCAATCAAGGAACACAACAGAATTTACCACCAGAA
CAGCGATATCAGTCGCAACTTGAGCAGCTTTCAGCTATGGGATTTGTAAATCCATTAATC
GCGACATTCGGAGACATAAATGCAGCAGTTGAACGATTGTTGGCATTGGGATCATTGTCA
TTAAGTTAACTTAATTAAATGGACGGTAAGATAAAGGAAGCAAAAGAATTAGAGTGGATG
ATATAAAAAATTTACCCTTTCCCAATCAACACAATATATATATATATATATACACATTTA
TTTCTATTGATCTTCTCATTCTCTTCAGTTATTCAAATAAGTTTATTTTATGAAAAAAAA
AAATACATTTCAAAATTTTCCTTTCTTATAATTTTTTCTTTTCTATAAATAATTATTTAG
AATATGAGACATTATTGCTAAATTTATATGATATGTAAATTAAAAAATGGGGAAAAAATA
TTTGGAGTTGAAA
>g3004.t10 Gene=g3004 Length=376
MDMQSRMQHELMGNPELMRTILDNPLVQQMLNNPDTMRTLITSNPQMQDLMQRNPEISHM
LNNPELLRQTMELARNPAMLQELMRSHDRAMSNLESVPGGYNALHRIYRDIQEPMLNAAS
GAFSSNPFSGLVDNGGSENPQQGSENREPLPNPWGGSGNQNSRPAPPPNNILNTPAMQSL
LQQMGENPEMMSTMMNAPYMRSMMEALSQDPNMAANLISQSPLLQANPQLQDQMRTMMPQ
LLQQMQNPEVQNMLSNPDALNAILQIQQGMEQLRQAAPGLVGTMGIPPPPPGTNQPPQTG
NTPNAPNQQLFNDFMQRMLNGMTNQGTQQNLPPEQRYQSQLEQLSAMGFVNPLIATFGDI
NAAVERLLALGSLSLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3004.t10 | Gene3D | G3DSA:1.10.260.100 | - | 46 | 100 | 2.0e-07 |
| 11 | g3004.t10 | Gene3D | G3DSA:1.10.8.10 | DNA helicase RuvA subunit | 320 | 374 | 0.0e+00 |
| 2 | g3004.t10 | PANTHER | PTHR10677 | UBIQUILIN | 1 | 163 | 0.0e+00 |
| 4 | g3004.t10 | PANTHER | PTHR10677:SF21 | UBIQUILIN-4 | 1 | 163 | 0.0e+00 |
| 1 | g3004.t10 | PANTHER | PTHR10677 | UBIQUILIN | 167 | 369 | 0.0e+00 |
| 3 | g3004.t10 | PANTHER | PTHR10677:SF21 | UBIQUILIN-4 | 167 | 369 | 0.0e+00 |
| 6 | g3004.t10 | SMART | SM00727 | CBM | 14 | 43 | 1.2e+01 |
| 8 | g3004.t10 | SMART | SM00727 | CBM | 44 | 83 | 0.0e+00 |
| 9 | g3004.t10 | SMART | SM00727 | CBM | 187 | 234 | 2.4e-05 |
| 7 | g3004.t10 | SMART | SM00727 | CBM | 238 | 270 | 6.0e-01 |
| 5 | g3004.t10 | SUPERFAMILY | SSF46934 | UBA-like | 322 | 368 | 0.0e+00 |
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 transcript has been annotated with K04523 (ubiquilin)
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. There were no conditions that were differentially expressed