General information for g12937.t29
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 26S proteasome non-ATPase regulatory subunit 4.
Parent gene
- The parent gene g12937 is located on chr_1: 27010180..27011251 (- 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_1 | g12937 | g12937.t29 | TTS | g12937.t29 | 27009496 | 27009496 |
| chr_1 | g12937 | g12937.t29 | isoform | g12937.t29 | 27009934 | 27011251 |
| chr_1 | g12937 | g12937.t29 | exon | g12937.t29.exon1 | 27009934 | 27010018 |
| chr_1 | g12937 | g12937.t29 | cds | g12937.t29.CDS1 | 27009935 | 27010018 |
| chr_1 | g12937 | g12937.t29 | exon | g12937.t29.exon2 | 27010151 | 27010699 |
| chr_1 | g12937 | g12937.t29 | cds | g12937.t29.CDS2 | 27010151 | 27010699 |
| chr_1 | g12937 | g12937.t29 | exon | g12937.t29.exon3 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t29 | cds | g12937.t29.CDS3 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t29 | exon | g12937.t29.exon4 | 27010930 | 27011251 |
| chr_1 | g12937 | g12937.t29 | cds | g12937.t29.CDS4 | 27010930 | 27010937 |
| chr_1 | g12937 | g12937.t29 | TSS | g12937.t29 | 27011325 | 27011325 |
Sequences
>g12937.t29 Gene=g12937 Length=1071
ATGGTTTTAGAAAGTACTATGATTTGGTGAGTAATAAAATTGATTAAAAGATGACATCAA
ATGTTTTGTATTAGAACCAAGCTATGATTGAAAGTTCTCAAAATACTCTTTTGTGATTCG
TGATTCAGCAAATTTGAATTTCTTAATAACCAAAATAAAACAAATTTCTTTGTCATTTTA
GCTTGGATAATAGCGATTATCAACGTAATGGAGATTATCTACCAACAAGATTGAACGCAC
AGAAGGATGGTATCAATTTAGTTTGTCTCACAAAATTAAGATCGAATCCAGAAAACAATG
TTGGTCTTTTAACAATGGCAAAAACTGTAGAAGTTTTAGCTACTCTGACTAGTGATGTAG
GACGAATTATGTCAAAGATGCATCTCGTTCAACCCAACGGAAATATTAATTTAGTAACTG
GAATTAGAATTGCTCATCTTGTTCTAAAACATCGTCAAGGCAAGAATCATAAAATGCGTA
TTGTACTTTTTATTGGATCACCACTTGAAGTGGATAAAGCTGAAATGGAAAAATTAGCTA
AGAAATTGAAGAAAGAAAAAGTTAATGTCGATATTGTGAGCTTTGGTGACCATCAAAAAA
ATAATGATGTGCTTACTTCATTTATTAATACATTGAATGGAAAAGATGGTACAGGTTCTC
ATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAAGAAGCATTAATTTCATCAGCAATCA
TTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGTGGTGCAGGCTTTGAATTTGGTGTTG
ATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTAAGAGTTTCAATGGAAGAACAGCGTC
AGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCAGCTTCTGCTCAAGAAACTTCAACTG
AAAATGCTCCAGCTGTTTCTACTATTGCACCAACATCTGACGAAGCTATGCTTGAACGTG
CACTCGCATTGTCGACTGAGACACCGAGTGACGAGGCTATGCCAGATTTTGCTAACATGA
CTGAAGAGGAACAAATTGCTTTTGCTATGCAAATGTCAATGCAAGATGCAC
>g12937.t29 Gene=g12937 Length=252
MAKTVEVLATLTSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFI
GSPLEVDKAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSV
PRGSQLQEALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEE
EQRRAQAASAQETSTENAPAVSTIAPTSDEAMLERALALSTETPSDEAMPDFANMTEEEQ
IAFAMQMSMQDA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g12937.t29 | Coils | Coil | Coil | 64 | 84 | - |
| 11 | g12937.t29 | Coils | Coil | Coil | 168 | 191 | - |
| 8 | g12937.t29 | Gene3D | G3DSA:3.40.50.410 | - | 1 | 133 | 3.8E-44 |
| 9 | g12937.t29 | Gene3D | G3DSA:1.10.10.890 | - | 208 | 250 | 3.6E-17 |
| 16 | g12937.t29 | MobiDBLite | mobidb-lite | consensus disorder prediction | 171 | 252 | - |
| 17 | g12937.t29 | MobiDBLite | mobidb-lite | consensus disorder prediction | 172 | 186 | - |
| 15 | g12937.t29 | MobiDBLite | mobidb-lite | consensus disorder prediction | 187 | 204 | - |
| 5 | g12937.t29 | PANTHER | PTHR10223:SF7 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 2 | 252 | 3.8E-97 |
| 6 | g12937.t29 | PANTHER | PTHR10223 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 2 | 252 | 3.8E-97 |
| 1 | g12937.t29 | Pfam | PF13519 | von Willebrand factor type A domain | 1 | 60 | 1.9E-7 |
| 2 | g12937.t29 | Pfam | PF02809 | Ubiquitin interaction motif | 159 | 174 | 0.0063 |
| 3 | g12937.t29 | Pfam | PF02809 | Ubiquitin interaction motif | 208 | 222 | 0.019 |
| 4 | g12937.t29 | Pfam | PF02809 | Ubiquitin interaction motif | 236 | 252 | 0.0013 |
| 18 | g12937.t29 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 158 | 177 | 10.732 |
| 19 | g12937.t29 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 236 | 252 | 9.665 |
| 13 | g12937.t29 | SMART | SM00726 | uim | 158 | 177 | 0.021 |
| 12 | g12937.t29 | SMART | SM00726 | uim | 208 | 227 | 0.84 |
| 14 | g12937.t29 | SMART | SM00726 | uim | 236 | 252 | 180.0 |
| 7 | g12937.t29 | SUPERFAMILY | SSF53300 | vWA-like | 3 | 124 | 3.42E-17 |
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 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.
