General information for g12937.t21
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.t21 | TTS | g12937.t21 | 27009496 | 27009496 |
| chr_1 | g12937 | g12937.t21 | isoform | g12937.t21 | 27009648 | 27011251 |
| chr_1 | g12937 | g12937.t21 | exon | g12937.t21.exon1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t21 | cds | g12937.t21.CDS1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t21 | exon | g12937.t21.exon2 | 27009934 | 27009999 |
| chr_1 | g12937 | g12937.t21 | cds | g12937.t21.CDS2 | 27009934 | 27009999 |
| chr_1 | g12937 | g12937.t21 | exon | g12937.t21.exon3 | 27010138 | 27010699 |
| chr_1 | g12937 | g12937.t21 | cds | g12937.t21.CDS3 | 27010138 | 27010699 |
| chr_1 | g12937 | g12937.t21 | exon | g12937.t21.exon4 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t21 | cds | g12937.t21.CDS4 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t21 | exon | g12937.t21.exon5 | 27010930 | 27011058 |
| chr_1 | g12937 | g12937.t21 | cds | g12937.t21.CDS5 | 27010930 | 27011058 |
| chr_1 | g12937 | g12937.t21 | exon | g12937.t21.exon6 | 27011226 | 27011251 |
| chr_1 | g12937 | g12937.t21 | cds | g12937.t21.CDS6 | 27011226 | 27011251 |
| chr_1 | g12937 | g12937.t21 | TSS | g12937.t21 | 27011325 | 27011325 |
Sequences
>g12937.t21 Gene=g12937 Length=1122
ATGGTTTTAGAAAGTACTATGATTTGCGATTATCAACGTAATGGAGATTATCTACCAACA
AGATTGAACGCACAGAAGGATGGTATCAATTTAGTTTGTCTCACAAAATTAAGATCGAAT
CCAGAAAACAATGTTGGTCTTTTAACAATGGCAAAAACTGTAGAAGTTTTAGCTACTCTG
ACTAGTGATGTAGGACGAATTATGTCAAAGATGCATCTCGTTCAACCCAACGGAAATATT
AATTTAGTAACTGGAATTAGAATTGCTCATCTTGTTCTAAAACATCGTCAAGGCAAGAAT
CATAAAATGCGTATTGTACTTTTTATTGGATCACCACTTGAAGTGGATAAAGCTGAAATG
GAAAAATTAGCTAAGAAATTGAAGAAAGAAAAAGTTAATGTCGATATTGTGAGCTTTGGT
GACCATCAAAAAAATAATGATGTGCTTACTTCATTTATTAATACATTGAATGGAAAAGAT
GGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAAGAAGCATTAATT
TCATCAGCAATCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGTGGTGCAGGCTTT
GAATTTGGTGTTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTAAGAGTTTCAATG
GAAGAACAGCGTCAGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCAGCTTCTGCTCAA
GAAACTTCAACTGAAAATGCTCCAGCTGTTTCTACTATTGCACCAACATCTGACGAAGCT
ATGCTTGAACGTGCACTCGCATTGTCGACTGAGACACCGGTAAAAAGACTTCATTTTGCT
AACATGACTGAAGAGGAACAAATTGCTTTTGCTATGCAAATGTCAATGCAAGATGCACAG
GAGCCTATAACACAACAAGCAAAACGTCCAAAAAAAGACGATACACCAATGGAAGTTGAT
GAAGATTATAATGAAGTAATTACTGATCCAGCATTTCTCCAGAGTGTTTTAGAAAATCTT
CCTGGTGTAGATCCGCAATCTGAGGCAATACGTGGTGCAGTTGACTCCTTAAATAAAGAC
AAAAAGTCTGATAAAGATGGAAAAGGCAGCGGATCTAAATAA
>g12937.t21 Gene=g12937 Length=373
MVLESTMICDYQRNGDYLPTRLNAQKDGINLVCLTKLRSNPENNVGLLTMAKTVEVLATL
TSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFIGSPLEVDKAEM
EKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSVPRGSQLQEALI
SSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEEEQRRAQAASAQ
ETSTENAPAVSTIAPTSDEAMLERALALSTETPVKRLHFANMTEEEQIAFAMQMSMQDAQ
EPITQQAKRPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQSEAIRGAVDSLNKD
KKSDKDGKGSGSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12937.t21 | Coils | Coil | Coil | 113 | 133 | - |
| 10 | g12937.t21 | Coils | Coil | Coil | 217 | 240 | - |
| 8 | g12937.t21 | Gene3D | G3DSA:3.40.50.410 | - | 3 | 182 | 7.7E-63 |
| 9 | g12937.t21 | Gene3D | G3DSA:1.10.10.890 | - | 257 | 297 | 9.1E-13 |
| 19 | g12937.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 220 | 256 | - |
| 15 | g12937.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 221 | 235 | - |
| 18 | g12937.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 236 | 253 | - |
| 17 | g12937.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 338 | 373 | - |
| 16 | g12937.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 354 | 373 | - |
| 5 | g12937.t21 | PANTHER | PTHR10223:SF7 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 8 | 368 | 6.6E-134 |
| 6 | g12937.t21 | PANTHER | PTHR10223 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 8 | 368 | 6.6E-134 |
| 1 | g12937.t21 | Pfam | PF13519 | von Willebrand factor type A domain | 13 | 109 | 5.8E-17 |
| 4 | g12937.t21 | Pfam | PF02809 | Ubiquitin interaction motif | 208 | 223 | 0.01 |
| 3 | g12937.t21 | Pfam | PF02809 | Ubiquitin interaction motif | 257 | 271 | 0.03 |
| 2 | g12937.t21 | Pfam | PF02809 | Ubiquitin interaction motif | 283 | 299 | 0.0022 |
| 21 | g12937.t21 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 207 | 226 | 10.732 |
| 20 | g12937.t21 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 257 | 276 | 8.566 |
| 22 | g12937.t21 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 283 | 302 | 10.363 |
| 13 | g12937.t21 | SMART | SM00726 | uim | 207 | 226 | 0.021 |
| 12 | g12937.t21 | SMART | SM00726 | uim | 257 | 276 | 4.4 |
| 14 | g12937.t21 | SMART | SM00726 | uim | 283 | 302 | 0.025 |
| 7 | g12937.t21 | SUPERFAMILY | SSF53300 | vWA-like | 13 | 173 | 2.05E-26 |
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 transcript has been annotated with K03029 (26S proteasome regulatory subunit N10)
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. There were no conditions that were differentially expressed