General information for g3004.t9
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.t9 | TSS | g3004.t9 | 21915593 | 21915593 |
| chr_3 | g3004 | g3004.t9 | isoform | g3004.t9 | 21916318 | 21916990 |
| chr_3 | g3004 | g3004.t9 | exon | g3004.t9.exon1 | 21916318 | 21916990 |
| chr_3 | g3004 | g3004.t9 | cds | g3004.t9.CDS1 | 21916528 | 21916989 |
| chr_3 | g3004 | g3004.t9 | TTS | g3004.t9 | NA | NA |
Sequences
>g3004.t9 Gene=g3004 Length=673
ACAGTTCATTTGGTAAGTTTATTATAGAATTAGGAAATGACCTAATTAAATTATTATCGT
TATTCACTTAAGGTTATCAAAGCTCCACCAAAACCTGAAGCAGAAGGTCCAACACGACGA
CCAGCAGACGTACGTCAAACACCATTCGGTTTAAATCAAATTGGTGGTCTATCAGGACTT
GAAGCGCTCGGTGCTAATTCAAGTACATTCATGGATATGCAATCTCGAATGCAGCATGAA
TTGATGGGGAATCCTGAGTTAATGAGAACAATTTTAGATAACCCCTTAGTTCAACAAATG
CTTAATAATCCAGACACAATGAGAACCTTAATTACGAGCAATCCTCAAATGCAAGATTTA
ATGCAGCGTAATCCAGAAATTTCTCACATGCTCAATAATCCCGAATTGTTGCGACAAACT
ATGGAACTTGCAAGGAATCCAGCTATGTTGCAAGAGTTGATGCGTTCACACGATAGAGCA
ATGTCTAATTTGGAATCAGTTCCAGGTGGTTATAATGCGCTACATCGCATTTATCGTGAT
ATTCAAGAGCCAATGCTGAATGCAGCTTCTGGAGCATTTTCATCAAACCCATTCAGTGGA
TTAGTTGATAATGGAGGTTCTGAGAATCCTCAACAAGGAAGTGAAAATCGTGAACCATTA
CCAAATCCATGGG
>g3004.t9 Gene=g3004 Length=154
MDMQSRMQHELMGNPELMRTILDNPLVQQMLNNPDTMRTLITSNPQMQDLMQRNPEISHM
LNNPELLRQTMELARNPAMLQELMRSHDRAMSNLESVPGGYNALHRIYRDIQEPMLNAAS
GAFSSNPFSGLVDNGGSENPQQGSENREPLPNPW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3004.t9 | Gene3D | G3DSA:1.10.260.100 | - | 46 | 100 | 4.8E-8 |
| 5 | g3004.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 131 | 154 | - |
| 1 | g3004.t9 | PANTHER | PTHR10677 | UBIQUILIN | 1 | 154 | 1.7E-68 |
| 2 | g3004.t9 | PANTHER | PTHR10677:SF21 | UBIQUILIN-4 | 1 | 154 | 1.7E-68 |
| 3 | g3004.t9 | SMART | SM00727 | CBM | 14 | 43 | 12.0 |
| 4 | g3004.t9 | SMART | SM00727 | CBM | 44 | 83 | 4.9E-8 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
