General information for g3004.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t12 | TSS | g3004.t12 | 21916190 | 21916190 |
| chr_3 | g3004 | g3004.t12 | isoform | g3004.t12 | 21916990 | 21918435 |
| chr_3 | g3004 | g3004.t12 | exon | g3004.t12.exon1 | 21916990 | 21917599 |
| chr_3 | g3004 | g3004.t12 | cds | g3004.t12.CDS1 | 21917056 | 21917599 |
| chr_3 | g3004 | g3004.t12 | exon | g3004.t12.exon2 | 21917663 | 21917755 |
| chr_3 | g3004 | g3004.t12 | cds | g3004.t12.CDS2 | 21917663 | 21917739 |
| chr_3 | g3004 | g3004.t12 | exon | g3004.t12.exon3 | 21918127 | 21918435 |
| chr_3 | g3004 | g3004.t12 | TTS | g3004.t12 | NA | NA |
Sequences
>g3004.t12 Gene=g3004 Length=1012
GGCGGTAGTGGAAATCAAAATTCCCGACCAGCTCCACCACCAAATAATATTTTAAACACT
CCAGCAATGCAAAGTCTTTTACAACAAATGGGAGAAAATCCTGAAATGATGTCAACTATG
ATGAATGCACCATATATGCGTTCAATGATGGAAGCACTTTCACAAGATCCGAATATGGCG
GCAAATTTGATTAGTCAAAGTCCTCTTCTTCAAGCAAATCCACAATTGCAAGATCAAATG
AGAACAATGATGCCGCAACTTTTACAGCAAATGCAAAATCCAGAAGTTCAAAATATGCTG
TCCAATCCTGATGCATTGAATGCAATCTTACAAATTCAACAAGGCATGGAACAACTTCGA
CAAGCGGCACCAGGATTAGTTGGAACCATGGGAATTCCACCACCTCCTCCCGGAACGAAT
CAGCCACCACAAACTGGAAACACACCGAATGCACCAAATCAACAACTTTTTAATGACTTT
ATGCAACGAATGCTTAATGGAATGACCAATCAAGGAACACAACAGAATTTACCACCAGAA
CAGCGATATCAGTCGCAACTTGAGCAGCTTTCAGCTATGGGATTTGTAAATCGTGAAGCC
AATTTACAAGCATTAATCGCGACATTCGGAGACATAAATGCAGCAGTTGAACGATTGTTG
GCATTGGGATCATTGTCATTAAGTTAACTTAATTAAATGGACGGACATTCTAGAAACCAG
GCGACTGAATAATCGTCATCTTTAAGTTATTCAATTTCGTATTAATTGCAAATTTCTTAT
TCGTTCTATAAAAACGTATATTTCATGTATAGAAAATTTAAATGTGCTTTGAATGGGGGA
TAAAATTAATGTAAAAATAAAAGAACTCAATTAAGTAAAGCCAGGAAAAAATCATTTTCT
AATTATATTCAACATTTTAATGTTCCGACCAACATAAGATTCAATCATCTTTTGAATAAG
CGCGTTGATTTCCATATTCCTAATTGTAAGAATTTTTAATTTTGTTGTCTCT
>g3004.t12 Gene=g3004 Length=206
MQSLLQQMGENPEMMSTMMNAPYMRSMMEALSQDPNMAANLISQSPLLQANPQLQDQMRT
MMPQLLQQMQNPEVQNMLSNPDALNAILQIQQGMEQLRQAAPGLVGTMGIPPPPPGTNQP
PQTGNTPNAPNQQLFNDFMQRMLNGMTNQGTQQNLPPEQRYQSQLEQLSAMGFVNREANL
QALIATFGDINAAVERLLALGSLSLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3004.t12 | CDD | cd14399 | UBA_PLICs | 160 | 196 | 1.0423E-15 |
| 5 | g3004.t12 | Gene3D | G3DSA:1.10.8.10 | DNA helicase RuvA subunit | 144 | 204 | 1.8E-24 |
| 2 | g3004.t12 | PANTHER | PTHR10677 | UBIQUILIN | 1 | 199 | 3.2E-53 |
| 3 | g3004.t12 | PANTHER | PTHR10677:SF21 | UBIQUILIN-4 | 1 | 199 | 3.2E-53 |
| 1 | g3004.t12 | Pfam | PF00627 | UBA/TS-N domain | 161 | 197 | 1.5E-8 |
| 7 | g3004.t12 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 50 | - |
| 8 | g3004.t12 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 37 | - |
| 9 | g3004.t12 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 38 | 45 | - |
| 10 | g3004.t12 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 46 | 50 | - |
| 6 | g3004.t12 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 51 | 206 | - |
| 15 | g3004.t12 | ProSiteProfiles | PS50030 | Ubiquitin-associated domain (UBA) profile. | 156 | 200 | 11.872 |
| 13 | g3004.t12 | SMART | SM00727 | CBM | 11 | 58 | 2.4E-5 |
| 14 | g3004.t12 | SMART | SM00727 | CBM | 62 | 94 | 0.6 |
| 12 | g3004.t12 | SMART | SM00165 | uba_6 | 161 | 199 | 1.5E-7 |
| 4 | g3004.t12 | SUPERFAMILY | SSF46934 | UBA-like | 146 | 198 | 2.43E-15 |
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.
