General information for g4493.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4493 is located on chr_2: 2885790..2886452 (- 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_2 | g4493 | g4493.t10 | TTS | g4493.t10 | 2885280 | 2885280 |
| chr_2 | g4493 | g4493.t10 | isoform | g4493.t10 | 2885341 | 2886452 |
| chr_2 | g4493 | g4493.t10 | exon | g4493.t10.exon1 | 2885341 | 2885765 |
| chr_2 | g4493 | g4493.t10 | cds | g4493.t10.CDS1 | 2885487 | 2885765 |
| chr_2 | g4493 | g4493.t10 | exon | g4493.t10.exon2 | 2885828 | 2886326 |
| chr_2 | g4493 | g4493.t10 | cds | g4493.t10.CDS2 | 2885828 | 2886326 |
| chr_2 | g4493 | g4493.t10 | exon | g4493.t10.exon3 | 2886403 | 2886452 |
| chr_2 | g4493 | g4493.t10 | cds | g4493.t10.CDS3 | 2886403 | 2886452 |
| chr_2 | g4493 | g4493.t10 | TSS | g4493.t10 | 2886450 | 2886450 |
Sequences
>g4493.t10 Gene=g4493 Length=974
ATGAGTGGCATTGAACAATTGGTCGAAATGGGTTTTCCAAGAGATAGAGCAGAAAAGGCA
TTAAGTTGCAATAATAATAATGTAGAACAAGCAATGGAATGGTTGTTAGTTCATAGTGAG
GATGATATGTCAAATGTTAATCCTCCAAATGAACCTAAGCCATTGGAAATAAAAAATGAT
GAGTCATCAAATGAACCTGCAGCAAATGCTACCACAAGTGAATCTGATCAAGCAATACCG
CAAGAAGCAAAGAGTATTAAGTGTGAAGACTGTGGTAAACTCTTCAAAACTACAATCGAA
ATAGAATTTCATGCAGCAAAATCTGGACATAGCAATTTCTCAGAATCTACAGAAGAGAAG
AAACCATTGACAGAAGAGGAGAAGAAAGCTCAATTAGCACAACTAGAAGAAAGAATAAAG
GCTAAACGTTTGGAACGAGAAGAACGTGAAAAACAAGAAGCATTAGAAAAGGAGCGGTTA
AGAATTAAGAGTGGTAAAGATATGAGTGAAGCTCGACGCAAATTGGAAGAAGAAGAAATG
AAAAAGATTAACAAAGAAAACGAGAAAAACAAGAAGAGAAAATTGCTAGAGAACGAGTTA
AGGCTCAAATTGAAGCAGATAAGGCAGCACGAAGAGCAAAAGCAGCAGGTCAACCACCGT
CAATATCAGAGCCAGTACAAGTACCAGTTCAAACACCACAAGTTACACCTCCACCAAAAG
ATTACAAAGAAACAAAAATACAGATTCGTTTGCCCAATGGTTCAACACTTGTTGAAACAT
TCGATAAAAGAGAGCAACTATCGGCTGTTAGATTGTTTATACAATTAAAGCAAGGTGATG
AACCTGGAACTTTCCCATTTGGCATGATGACAAACTTTCCACGTAAAGTTTTCACTGAAG
AAGACTATGAAAAAAGCTTAGATGAACTAAAACTTGTTCCATCAGCAGTTATTATTGTCA
CAAAGACTGCATAA
>g4493.t10 Gene=g4493 Length=275
MSGIEQLVEMGFPRDRAEKALSCNNNNVEQAMEWLLVHSEDDMSNVNPPNEPKPLEIKND
ESSNEPAANATTSESDQAIPQEAKSIKCEDCGKLFKTTIEIEFHAAKSGHSNFSESTEEK
KPLTEEEKKAQLAQLEERIKAKRLEREEREKQEALEKERLRIKSGKDMSEARRKLEEEEM
KKINKENEKNKKRKLLENELRLKLKQIRQHEEQKQQVNHRQYQSQYKYQFKHHKLHLHQK
ITKKQKYRFVCPMVQHLLKHSIKESNYRLLDCLYN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4493.t10 | CDD | cd14302 | UBA_UBXN1 | 2 | 41 | 4.23394E-16 |
| 5 | g4493.t10 | Coils | Coil | Coil | 125 | 161 | - |
| 6 | g4493.t10 | Coils | Coil | Coil | 166 | 220 | - |
| 4 | g4493.t10 | Gene3D | G3DSA:1.10.8.10 | DNA helicase RuvA subunit | 1 | 83 | 5.5E-17 |
| 12 | g4493.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 39 | 84 | - |
| 13 | g4493.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 62 | 80 | - |
| 10 | g4493.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 109 | 130 | - |
| 11 | g4493.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 130 | - |
| 2 | g4493.t10 | PANTHER | PTHR46340 | UBX DOMAIN-CONTAINING PROTEIN 1 | 1 | 228 | 4.1E-56 |
| 1 | g4493.t10 | Pfam | PF00627 | UBA/TS-N domain | 4 | 35 | 1.9E-12 |
| 9 | g4493.t10 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 88 | 110 | - |
| 14 | g4493.t10 | ProSiteProfiles | PS50030 | Ubiquitin-associated domain (UBA) profile. | 1 | 38 | 15.005 |
| 15 | g4493.t10 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 86 | 115 | 8.663 |
| 8 | g4493.t10 | SMART | SM00165 | uba_6 | 4 | 37 | 3.7E-8 |
| 3 | g4493.t10 | SUPERFAMILY | SSF46934 | UBA-like | 4 | 42 | 1.82E-14 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
