General information for g12937.t28
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.t28 | TTS | g12937.t28 | 27009496 | 27009496 |
| chr_1 | g12937 | g12937.t28 | isoform | g12937.t28 | 27009648 | 27011251 |
| chr_1 | g12937 | g12937.t28 | exon | g12937.t28.exon1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t28 | cds | g12937.t28.CDS1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t28 | exon | g12937.t28.exon2 | 27009934 | 27010018 |
| chr_1 | g12937 | g12937.t28 | cds | g12937.t28.CDS2 | 27009934 | 27010018 |
| chr_1 | g12937 | g12937.t28 | exon | g12937.t28.exon3 | 27010151 | 27010699 |
| chr_1 | g12937 | g12937.t28 | cds | g12937.t28.CDS3 | 27010151 | 27010699 |
| chr_1 | g12937 | g12937.t28 | exon | g12937.t28.exon4 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t28 | cds | g12937.t28.CDS4 | 27010752 | 27010811 |
| chr_1 | g12937 | g12937.t28 | exon | g12937.t28.exon5 | 27010940 | 27011070 |
| chr_1 | g12937 | g12937.t28 | exon | g12937.t28.exon6 | 27011226 | 27011251 |
| chr_1 | g12937 | g12937.t28 | TSS | g12937.t28 | 27011325 | 27011325 |
Sequences
>g12937.t28 Gene=g12937 Length=1130
ATGGTTTTAGAAAGTACTATGATTTGCTTGGATAATAGCGATTATCAACGTAATGGAGAT
TATCTACCAACAAGATTGAACGCACAGAAGGATGGTATCAATTTAGTTTGTCTCACAAAA
TTAAGATCGAATCCAGAAAACAATGTTGGTCTTTTAAAACTGTAGAAGTTTTAGCTACTC
TGACTAGTGATGTAGGACGAATTATGTCAAAGATGCATCTCGTTCAACCCAACGGAAATA
TTAATTTAGTAACTGGAATTAGAATTGCTCATCTTGTTCTAAAACATCGTCAAGGCAAGA
ATCATAAAATGCGTATTGTACTTTTTATTGGATCACCACTTGAAGTGGATAAAGCTGAAA
TGGAAAAATTAGCTAAGAAATTGAAGAAAGAAAAAGTTAATGTCGATATTGTGAGCTTTG
GTGACCATCAAAAAAATAATGATGTGCTTACTTCATTTATTAATACATTGAATGGAAAAG
ATGGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAAGAAGCATTAA
TTTCATCAGCAATCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGTGGTGCAGGCT
TTGAATTTGGTGTTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTAAGAGTTTCAA
TGGAAGAACAGCGTCAGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCAGCTTCTGCTC
AAGAAACTTCAACTGAAAATGCTCCAGCTGTTTCTACTATTGCACCAACATCTGACGAAG
CTATGCTTGAACGTGCACTCGCATTGTCGACTGAGACACCGAGTGACGAGGCTATGCCAG
ATTTTGCTAACATGACTGAAGAGGAACAAATTGCTTTTGCTATGCAAATGTCAATGCAAG
ATGCACAGGAGCCTATAACACAACAAGCAAAACGTCCAAAAAAAGACGATACACCAATGG
AAGTTGATGAAGATTATAATGAAGTAATTACTGATCCAGCATTTCTCCAGAGTGTTTTAG
AAAATCTTCCTGGTGTAGATCCGCAATCTGAGGCAATACGTGGTGCAGTTGACTCCTTAA
ATAAAGACAAAAAGTCTGATAAAGATGGAAAAGGCAGCGGATCTAAATAA
>g12937.t28 Gene=g12937 Length=305
MHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFIGSPLEVDKAEMEKLAKKLKKE
KVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSVPRGSQLQEALISSAIIQGEDG
MGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEEEQRRAQAASAQETSTENAPAV
STIAPTSDEAMLERALALSTETPSDEAMPDFANMTEEEQIAFAMQMSMQDAQEPITQQAK
RPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQSEAIRGAVDSLNKDKKSDKDGK
GSGSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g12937.t28 | Coils | Coil | Coil | 43 | 63 | - |
| 9 | g12937.t28 | Coils | Coil | Coil | 147 | 170 | - |
| 7 | g12937.t28 | Gene3D | G3DSA:3.40.50.410 | - | 1 | 112 | 4.0E-36 |
| 8 | g12937.t28 | Gene3D | G3DSA:1.10.10.890 | - | 187 | 229 | 4.8E-17 |
| 19 | g12937.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 150 | 187 | - |
| 18 | g12937.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 151 | 165 | - |
| 17 | g12937.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 166 | 183 | - |
| 15 | g12937.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 231 | 251 | - |
| 14 | g12937.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 269 | 305 | - |
| 16 | g12937.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 286 | 305 | - |
| 4 | g12937.t28 | PANTHER | PTHR10223:SF7 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 1 | 300 | 6.4E-104 |
| 5 | g12937.t28 | PANTHER | PTHR10223 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 1 | 300 | 6.4E-104 |
| 2 | g12937.t28 | Pfam | PF02809 | Ubiquitin interaction motif | 138 | 153 | 0.008 |
| 1 | g12937.t28 | Pfam | PF02809 | Ubiquitin interaction motif | 187 | 201 | 0.024 |
| 3 | g12937.t28 | Pfam | PF02809 | Ubiquitin interaction motif | 215 | 231 | 0.0017 |
| 20 | g12937.t28 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 137 | 156 | 10.732 |
| 21 | g12937.t28 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 215 | 234 | 10.363 |
| 11 | g12937.t28 | SMART | SM00726 | uim | 137 | 156 | 0.021 |
| 13 | g12937.t28 | SMART | SM00726 | uim | 187 | 206 | 0.84 |
| 12 | g12937.t28 | SMART | SM00726 | uim | 215 | 234 | 0.025 |
| 6 | g12937.t28 | SUPERFAMILY | SSF53300 | vWA-like | 2 | 103 | 2.4E-13 |
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