General information for g4493.t11
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.t11 | TTS | g4493.t11 | 2885280 | 2885280 |
| chr_2 | g4493 | g4493.t11 | isoform | g4493.t11 | 2885341 | 2886452 |
| chr_2 | g4493 | g4493.t11 | exon | g4493.t11.exon1 | 2885341 | 2885769 |
| chr_2 | g4493 | g4493.t11 | cds | g4493.t11.CDS1 | 2885341 | 2885769 |
| chr_2 | g4493 | g4493.t11 | exon | g4493.t11.exon2 | 2885828 | 2886452 |
| chr_2 | g4493 | g4493.t11 | cds | g4493.t11.CDS2 | 2885828 | 2886283 |
| chr_2 | g4493 | g4493.t11 | TSS | g4493.t11 | 2886450 | 2886450 |
Sequences
>g4493.t11 Gene=g4493 Length=1054
ATGAGTGGCATTGAACAATTGGTCGAAATGGGTTTTCCAAGAGATAGAGCGTAAGTTTAG
CGTACTTTTCAATATAATAATATGTTTTTGAATTGAAAAAAAAATGTAAAAATATTTATT
TTACAGAGAAAAGGCATTAAGTTGCAATAATAATAATGTAGAACAAGCAATGGAATGGTT
GTTAGTTCATAGTGAGGATGATATGTCAAATGTTAATCCTCCAAATGAACCTAAGCCATT
GGAAATAAAAAATGATGAGTCATCAAATGAACCTGCAGCAAATGCTACCACAAGTGAATC
TGATCAAGCAATACCGCAAGAAGCAAAGAGTATTAAGTGTGAAGACTGTGGTAAACTCTT
CAAAACTACAATCGAAATAGAATTTCATGCAGCAAAATCTGGACATAGCAATTTCTCAGA
ATCTACAGAAGAGAAGAAACCATTGACAGAAGAGGAGAAGAAAGCTCAATTAGCACAACT
AGAAGAAAGAATAAAGGCTAAACGTTTGGAACGAGAAGAACGTGAAAAACAAGAAGCATT
AGAAAAGGAGCGGTTAAGAATTAAGAGTGGTAAAGATATGAGTGAAGCTCGACGCAAATT
GGAAGAAGAAGAAATGAAAAAGATTGTAGAACAAAGAAAACGAGAAAAACAAGAAGAGAA
AATTGCTAGAGAACGAGTTAAGGCTCAAATTGAAGCAGATAAGGCAGCACGAAGAGCAAA
AGCAGCAGGTCAACCACCGTCAATATCAGAGCCAGTACAAGTACCAGTTCAAACACCACA
AGTTACACCTCCACCAAAAGATTACAAAGAAACAAAAATACAGATTCGTTTGCCCAATGG
TTCAACACTTGTTGAAACATTCGATAAAAGAGAGCAACTATCGGCTGTTAGATTGTTTAT
ACAATTAAAGCAAGGTGATGAACCTGGAACTTTCCCATTTGGCATGATGACAAACTTTCC
ACGTAAAGTTTTCACTGAAGAAGACTATGAAAAAAGCTTAGATGAACTAAAACTTGTTCC
ATCAGCAGTTATTATTGTCACAAAGACTGCATAA
>g4493.t11 Gene=g4493 Length=294
MEWLLVHSEDDMSNVNPPNEPKPLEIKNDESSNEPAANATTSESDQAIPQEAKSIKCEDC
GKLFKTTIEIEFHAAKSGHSNFSESTEEKKPLTEEEKKAQLAQLEERIKAKRLEREEREK
QEALEKERLRIKSGKDMSEARRKLEEEEMKKIVEQRKREKQEEKIARERVKAQIEADKAA
RRAKAAGQPPSISEPVQVPVQTPQVTPPPKDYKETKIQIRLPNGSTLVETFDKREQLSAV
RLFIQLKQGDEPGTFPFGMMTNFPRKVFTEEDYEKSLDELKLVPSAVIIVTKTA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4493.t11 | Coils | Coil | Coil | 94 | 130 | - |
| 6 | g4493.t11 | Coils | Coil | Coil | 135 | 173 | - |
| 4 | g4493.t11 | Gene3D | G3DSA:3.10.20.90 | - | 208 | 292 | 3.4E-25 |
| 11 | g4493.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 54 | - |
| 13 | g4493.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 31 | 49 | - |
| 12 | g4493.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 75 | 99 | - |
| 14 | g4493.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 82 | 99 | - |
| 10 | g4493.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 143 | - |
| 9 | g4493.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 176 | 214 | - |
| 2 | g4493.t11 | PANTHER | PTHR46340 | UBX DOMAIN-CONTAINING PROTEIN 1 | 1 | 292 | 3.7E-93 |
| 1 | g4493.t11 | Pfam | PF00789 | UBX domain | 210 | 291 | 3.2E-22 |
| 7 | g4493.t11 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 57 | 79 | - |
| 16 | g4493.t11 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 55 | 84 | 8.663 |
| 15 | g4493.t11 | ProSiteProfiles | PS50033 | UBX domain profile. | 210 | 290 | 22.756 |
| 8 | g4493.t11 | SMART | SM00166 | ubx_3 | 207 | 292 | 5.2E-23 |
| 3 | g4493.t11 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 159 | 292 | 8.01E-29 |
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.
