General information for g4493.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative UBX domain-containing protein 1.
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.t1 | TTS | g4493.t1 | 2885280 | 2885280 |
| chr_2 | g4493 | g4493.t1 | isoform | g4493.t1 | 2885341 | 2886452 |
| chr_2 | g4493 | g4493.t1 | exon | g4493.t1.exon1 | 2885341 | 2885769 |
| chr_2 | g4493 | g4493.t1 | cds | g4493.t1.CDS1 | 2885341 | 2885769 |
| chr_2 | g4493 | g4493.t1 | exon | g4493.t1.exon2 | 2885828 | 2886326 |
| chr_2 | g4493 | g4493.t1 | cds | g4493.t1.CDS2 | 2885828 | 2886326 |
| chr_2 | g4493 | g4493.t1 | exon | g4493.t1.exon3 | 2886403 | 2886452 |
| chr_2 | g4493 | g4493.t1 | cds | g4493.t1.CDS3 | 2886403 | 2886452 |
| chr_2 | g4493 | g4493.t1 | TSS | g4493.t1 | 2886450 | 2886450 |
Sequences
>g4493.t1 Gene=g4493 Length=978
ATGAGTGGCATTGAACAATTGGTCGAAATGGGTTTTCCAAGAGATAGAGCAGAAAAGGCA
TTAAGTTGCAATAATAATAATGTAGAACAAGCAATGGAATGGTTGTTAGTTCATAGTGAG
GATGATATGTCAAATGTTAATCCTCCAAATGAACCTAAGCCATTGGAAATAAAAAATGAT
GAGTCATCAAATGAACCTGCAGCAAATGCTACCACAAGTGAATCTGATCAAGCAATACCG
CAAGAAGCAAAGAGTATTAAGTGTGAAGACTGTGGTAAACTCTTCAAAACTACAATCGAA
ATAGAATTTCATGCAGCAAAATCTGGACATAGCAATTTCTCAGAATCTACAGAAGAGAAG
AAACCATTGACAGAAGAGGAGAAGAAAGCTCAATTAGCACAACTAGAAGAAAGAATAAAG
GCTAAACGTTTGGAACGAGAAGAACGTGAAAAACAAGAAGCATTAGAAAAGGAGCGGTTA
AGAATTAAGAGTGGTAAAGATATGAGTGAAGCTCGACGCAAATTGGAAGAAGAAGAAATG
AAAAAGATTGTAGAACAAAGAAAACGAGAAAAACAAGAAGAGAAAATTGCTAGAGAACGA
GTTAAGGCTCAAATTGAAGCAGATAAGGCAGCACGAAGAGCAAAAGCAGCAGGTCAACCA
CCGTCAATATCAGAGCCAGTACAAGTACCAGTTCAAACACCACAAGTTACACCTCCACCA
AAAGATTACAAAGAAACAAAAATACAGATTCGTTTGCCCAATGGTTCAACACTTGTTGAA
ACATTCGATAAAAGAGAGCAACTATCGGCTGTTAGATTGTTTATACAATTAAAGCAAGGT
GATGAACCTGGAACTTTCCCATTTGGCATGATGACAAACTTTCCACGTAAAGTTTTCACT
GAAGAAGACTATGAAAAAAGCTTAGATGAACTAAAACTTGTTCCATCAGCAGTTATTATT
GTCACAAAGACTGCATAA
>g4493.t1 Gene=g4493 Length=325
MSGIEQLVEMGFPRDRAEKALSCNNNNVEQAMEWLLVHSEDDMSNVNPPNEPKPLEIKND
ESSNEPAANATTSESDQAIPQEAKSIKCEDCGKLFKTTIEIEFHAAKSGHSNFSESTEEK
KPLTEEEKKAQLAQLEERIKAKRLEREEREKQEALEKERLRIKSGKDMSEARRKLEEEEM
KKIVEQRKREKQEEKIARERVKAQIEADKAARRAKAAGQPPSISEPVQVPVQTPQVTPPP
KDYKETKIQIRLPNGSTLVETFDKREQLSAVRLFIQLKQGDEPGTFPFGMMTNFPRKVFT
EEDYEKSLDELKLVPSAVIIVTKTA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4493.t1 | CDD | cd14302 | UBA_UBXN1 | 2 | 41 | 3.97405E-16 |
| 9 | g4493.t1 | Coils | Coil | Coil | 125 | 161 | - |
| 8 | g4493.t1 | Coils | Coil | Coil | 166 | 204 | - |
| 7 | g4493.t1 | Gene3D | G3DSA:1.10.8.10 | DNA helicase RuvA subunit | 1 | 82 | 5.1E-17 |
| 6 | g4493.t1 | Gene3D | G3DSA:3.10.20.90 | - | 239 | 323 | 4.1E-25 |
| 17 | g4493.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 39 | 84 | - |
| 18 | g4493.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 62 | 80 | - |
| 14 | g4493.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 107 | 130 | - |
| 16 | g4493.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 130 | - |
| 15 | g4493.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 207 | 243 | - |
| 3 | g4493.t1 | PANTHER | PTHR46340 | UBX DOMAIN-CONTAINING PROTEIN 1 | 1 | 323 | 3.9E-109 |
| 2 | g4493.t1 | Pfam | PF00627 | UBA/TS-N domain | 4 | 35 | 2.4E-12 |
| 1 | g4493.t1 | Pfam | PF00789 | UBX domain | 241 | 322 | 3.9E-22 |
| 13 | g4493.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 88 | 110 | - |
| 20 | g4493.t1 | ProSiteProfiles | PS50030 | Ubiquitin-associated domain (UBA) profile. | 1 | 38 | 15.005 |
| 21 | g4493.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 86 | 115 | 8.663 |
| 19 | g4493.t1 | ProSiteProfiles | PS50033 | UBX domain profile. | 241 | 321 | 22.756 |
| 11 | g4493.t1 | SMART | SM00165 | uba_6 | 4 | 37 | 3.7E-8 |
| 12 | g4493.t1 | SMART | SM00166 | ubx_3 | 238 | 323 | 5.2E-23 |
| 5 | g4493.t1 | SUPERFAMILY | SSF46934 | UBA-like | 4 | 42 | 2.45E-14 |
| 4 | g4493.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 190 | 323 | 1.03E-28 |
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 K24348 (UBX domain-containing protein 1/4)
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.
