General information for g12937.t20
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.t20 | TTS | g12937.t20 | 27009496 | 27009496 |
| chr_1 | g12937 | g12937.t20 | isoform | g12937.t20 | 27009648 | 27011251 |
| chr_1 | g12937 | g12937.t20 | exon | g12937.t20.exon1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t20 | cds | g12937.t20.CDS1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t20 | exon | g12937.t20.exon2 | 27009934 | 27010018 |
| chr_1 | g12937 | g12937.t20 | cds | g12937.t20.CDS2 | 27009934 | 27010018 |
| chr_1 | g12937 | g12937.t20 | exon | g12937.t20.exon3 | 27010151 | 27010699 |
| chr_1 | g12937 | g12937.t20 | cds | g12937.t20.CDS3 | 27010151 | 27010699 |
| chr_1 | g12937 | g12937.t20 | exon | g12937.t20.exon4 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t20 | cds | g12937.t20.CDS4 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t20 | exon | g12937.t20.exon5 | 27011185 | 27011251 |
| chr_1 | g12937 | g12937.t20 | cds | g12937.t20.CDS5 | 27011185 | 27011201 |
| chr_1 | g12937 | g12937.t20 | TSS | g12937.t20 | 27011325 | 27011325 |
Sequences
>g12937.t20 Gene=g12937 Length=1040
ATGGTTTTAGAAAGTACTATGATTTGGTGAGTAATAAAATTGATTAAAAGATGACATCAA
ATGTTTTAACTGTAGAAGTTTTAGCTACTCTGACTAGTGATGTAGGACGAATTATGTCAA
AGATGCATCTCGTTCAACCCAACGGAAATATTAATTTAGTAACTGGAATTAGAATTGCTC
ATCTTGTTCTAAAACATCGTCAAGGCAAGAATCATAAAATGCGTATTGTACTTTTTATTG
GATCACCACTTGAAGTGGATAAAGCTGAAATGGAAAAATTAGCTAAGAAATTGAAGAAAG
AAAAAGTTAATGTCGATATTGTGAGCTTTGGTGACCATCAAAAAAATAATGATGTGCTTA
CTTCATTTATTAATACATTGAATGGAAAAGATGGTACAGGTTCTCATTTAGTTAGCGTTC
CAAGAGGATCACAATTGCAAGAAGCATTAATTTCATCAGCAATCATTCAAGGAGAAGATG
GAATGGGCGCAGGAATTGGTGGTGCAGGCTTTGAATTTGGTGTTGATCCTAATGAGGATC
CAGAACTTGCTCTTGCTTTAAGAGTTTCAATGGAAGAACAGCGTCAGCGACAAGAAGAAG
AGCAAAGACGTGCACAAGCAGCTTCTGCTCAAGAAACTTCAACTGAAAATGCTCCAGCTG
TTTCTACTATTGCACCAACATCTGACGAAGCTATGCTTGAACGTGCACTCGCATTGTCGA
CTGAGACACCGAGTGACGAGGCTATGCCAGATTTTGCTAACATGACTGAAGAGGAACAAA
TTGCTTTTGCTATGCAAATGTCAATGCAAGATGCACAGGAGCCTATAACACAACAAGCAA
AACGTCCAAAAAAAGACGATACACCAATGGAAGTTGATGAAGATTATAATGAAGTAATTA
CTGATCCAGCATTTCTCCAGAGTGTTTTAGAAAATCTTCCTGGTGTAGATCCGCAATCTG
AGGCAATACGTGGTGCAGTTGACTCCTTAAATAAAGACAAAAAGTCTGATAAAGATGGAA
AAGGCAGCGGATCTAAATAA
>g12937.t20 Gene=g12937 Length=329
MTSNVLTVEVLATLTSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIV
LFIGSPLEVDKAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHL
VSVPRGSQLQEALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQR
QEEEQRRAQAASAQETSTENAPAVSTIAPTSDEAMLERALALSTETPSDEAMPDFANMTE
EEQIAFAMQMSMQDAQEPITQQAKRPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVD
PQSEAIRGAVDSLNKDKKSDKDGKGSGSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g12937.t20 | Coils | Coil | Coil | 67 | 87 | - |
| 11 | g12937.t20 | Coils | Coil | Coil | 171 | 194 | - |
| 8 | g12937.t20 | Gene3D | G3DSA:3.40.50.410 | - | 1 | 136 | 2.4E-43 |
| 9 | g12937.t20 | Gene3D | G3DSA:1.10.10.890 | - | 211 | 253 | 5.3E-17 |
| 18 | g12937.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 211 | - |
| 15 | g12937.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 175 | 189 | - |
| 20 | g12937.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 207 | - |
| 19 | g12937.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 255 | 275 | - |
| 17 | g12937.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 293 | 329 | - |
| 16 | g12937.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 310 | 329 | - |
| 5 | g12937.t20 | PANTHER | PTHR10223:SF7 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 8 | 324 | 6.3E-113 |
| 6 | g12937.t20 | PANTHER | PTHR10223 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 8 | 324 | 6.3E-113 |
| 1 | g12937.t20 | Pfam | PF13519 | von Willebrand factor type A domain | 7 | 63 | 9.7E-7 |
| 4 | g12937.t20 | Pfam | PF02809 | Ubiquitin interaction motif | 162 | 177 | 0.0088 |
| 2 | g12937.t20 | Pfam | PF02809 | Ubiquitin interaction motif | 211 | 225 | 0.026 |
| 3 | g12937.t20 | Pfam | PF02809 | Ubiquitin interaction motif | 239 | 255 | 0.0019 |
| 22 | g12937.t20 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 161 | 180 | 10.732 |
| 21 | g12937.t20 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 239 | 258 | 10.363 |
| 14 | g12937.t20 | SMART | SM00726 | uim | 161 | 180 | 0.021 |
| 13 | g12937.t20 | SMART | SM00726 | uim | 211 | 230 | 0.84 |
| 12 | g12937.t20 | SMART | SM00726 | uim | 239 | 258 | 0.025 |
| 7 | g12937.t20 | SUPERFAMILY | SSF53300 | vWA-like | 8 | 127 | 7.53E-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. There were no conditions that were differentially expressed