General information for g12937.t13
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.t13 | TTS | g12937.t13 | 27009496 | 27009496 |
| chr_1 | g12937 | g12937.t13 | isoform | g12937.t13 | 27009648 | 27011251 |
| chr_1 | g12937 | g12937.t13 | exon | g12937.t13.exon1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t13 | cds | g12937.t13.CDS1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t13 | exon | g12937.t13.exon2 | 27009934 | 27010018 |
| chr_1 | g12937 | g12937.t13 | cds | g12937.t13.CDS2 | 27009934 | 27010018 |
| chr_1 | g12937 | g12937.t13 | exon | g12937.t13.exon3 | 27010151 | 27010677 |
| chr_1 | g12937 | g12937.t13 | cds | g12937.t13.CDS3 | 27010151 | 27010663 |
| chr_1 | g12937 | g12937.t13 | exon | g12937.t13.exon4 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t13 | exon | g12937.t13.exon5 | 27010930 | 27011070 |
| chr_1 | g12937 | g12937.t13 | exon | g12937.t13.exon6 | 27011226 | 27011251 |
| chr_1 | g12937 | g12937.t13 | TSS | g12937.t13 | 27011325 | 27011325 |
Sequences
>g12937.t13 Gene=g12937 Length=1118
ATGGTTTTAGAAAGTACTATGATTTGCTTGGATAATAGCGATTATCAACGTAATGGAGAT
TATCTACCAACAAGATTGAACGCACAGAAGGATGGTATCAATTTAGTTTGTCTCACAAAA
TTAAGATCGAATCCAGAAAACAATGTTGGTCTTTTAACAATGGCAAAAACTGTAGAAGTT
TTAGCTACTCTGACTAGTGATGTAGGACGAATTATGTCAAAGATGCATCTCGTTCAACCC
AACGGAAATATTAATTTAGTAACTGGAATTAGAATTGCTCATGCAAGAATCATAAAATGC
GTATTGTACTTTTTATTGGATCACCACTTGAAGTGGATAAAGCTGAAATGGAAAAATTAG
CTAAGAAATTGAAGAAAGAAAAAGTTAATGTCGATATTGTGAGCTTTGGTGACCATCAAA
AAAATAATGATGTGCTTACTTCATTTATTAATACATTGAATGGAAAAGATGGTACAGGTT
CTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAAGAAGCATTAATTTCATCAGCAA
TCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGTGGTGCAGGCTTTGAATTTGGTG
TTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTAAGAGTTTCAATGGAAGAACAGC
GTCAGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCAGCTTCTGCTCAAGAAACTTCAA
CTGAAAATGCTCCAGCTGTTTCTACTATTGCACCAACATCTGACGAAGCTATGCTTGAAC
GTGCACTCGCATTGTCGACTGAGACACCGAGTGACGAGGCTATGCCAGATTTTGCTAACA
TGACTGAAGAGGAACAAATTGCTTTTGCTATGCAAATGTCAATGCAAGATGCACAGGAGC
CTATAACACAACAAGCAAAACGTCCAAAAAAAGACGATACACCAATGGAAGTTGATGAAG
ATTATAATGAAGTAATTACTGATCCAGCATTTCTCCAGAGTGTTTTAGAAAATCTTCCTG
GTGTAGATCCGCAATCTGAGGCAATACGTGGTGCAGTTGACTCCTTAAATAAAGACAAAA
AGTCTGATAAAGATGGAAAAGGCAGCGGATCTAAATAA
>g12937.t13 Gene=g12937 Length=273
MRIVLFIGSPLEVDKAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGT
GSHLVSVPRGSQLQEALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEE
QRQRQEEEQRRAQAASAQETSTENAPAVSTIAPTSDEAMLERALALSTETPSDEAMPDFA
NMTEEEQIAFAMQMSMQDAQEPITQQAKRPKKDDTPMEVDEDYNEVITDPAFLQSVLENL
PGVDPQSEAIRGAVDSLNKDKKSDKDGKGSGSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g12937.t13 | Coils | Coil | Coil | 11 | 31 | - |
| 17 | g12937.t13 | Coils | Coil | Coil | 115 | 138 | - |
| 15 | g12937.t13 | Gene3D | G3DSA:3.40.50.410 | - | 1 | 80 | 2.0E-22 |
| 16 | g12937.t13 | Gene3D | G3DSA:1.10.10.890 | - | 155 | 197 | 4.0E-17 |
| 14 | g12937.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 155 | - |
| 13 | g12937.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 119 | 133 | - |
| 10 | g12937.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 134 | 151 | - |
| 9 | g12937.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 199 | 219 | - |
| 12 | g12937.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 237 | 273 | - |
| 11 | g12937.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 254 | 273 | - |
| 4 | g12937.t13 | PANTHER | PTHR10223:SF7 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 1 | 268 | 4.1E-84 |
| 5 | g12937.t13 | PANTHER | PTHR10223 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 1 | 268 | 4.1E-84 |
| 3 | g12937.t13 | Pfam | PF02809 | Ubiquitin interaction motif | 106 | 121 | 0.007 |
| 1 | g12937.t13 | Pfam | PF02809 | Ubiquitin interaction motif | 155 | 169 | 0.021 |
| 2 | g12937.t13 | Pfam | PF02809 | Ubiquitin interaction motif | 183 | 199 | 0.0015 |
| 19 | g12937.t13 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 105 | 124 | 10.732 |
| 20 | g12937.t13 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 183 | 202 | 10.363 |
| 7 | g12937.t13 | SMART | SM00726 | uim | 105 | 124 | 0.021 |
| 6 | g12937.t13 | SMART | SM00726 | uim | 155 | 174 | 0.84 |
| 8 | g12937.t13 | SMART | SM00726 | uim | 183 | 202 | 0.025 |
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.
