Gene loci information

Transcript annotation

  • This transcript has been annotated as 26S proteasome non-ATPase regulatory subunit 4.

Parent gene

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.t19 TTS g12937.t19 27009496 27009496
chr_1 g12937 g12937.t19 isoform g12937.t19 27009648 27011251
chr_1 g12937 g12937.t19 exon g12937.t19.exon1 27009648 27009871
chr_1 g12937 g12937.t19 cds g12937.t19.CDS1 27009648 27009871
chr_1 g12937 g12937.t19 exon g12937.t19.exon2 27009934 27010018
chr_1 g12937 g12937.t19 cds g12937.t19.CDS2 27009934 27010018
chr_1 g12937 g12937.t19 exon g12937.t19.exon3 27010151 27010224
chr_1 g12937 g12937.t19 cds g12937.t19.CDS3 27010151 27010224
chr_1 g12937 g12937.t19 exon g12937.t19.exon4 27010300 27010699
chr_1 g12937 g12937.t19 cds g12937.t19.CDS4 27010300 27010699
chr_1 g12937 g12937.t19 exon g12937.t19.exon5 27010752 27010866
chr_1 g12937 g12937.t19 cds g12937.t19.CDS5 27010752 27010866
chr_1 g12937 g12937.t19 exon g12937.t19.exon6 27010930 27011070
chr_1 g12937 g12937.t19 cds g12937.t19.CDS6 27010930 27011070
chr_1 g12937 g12937.t19 exon g12937.t19.exon7 27011226 27011251
chr_1 g12937 g12937.t19 cds g12937.t19.CDS7 27011226 27011251
chr_1 g12937 g12937.t19 TSS g12937.t19 27011325 27011325

Sequences

>g12937.t19 Gene=g12937 Length=1065
ATGGTTTTAGAAAGTACTATGATTTGCTTGGATAATAGCGATTATCAACGTAATGGAGAT
TATCTACCAACAAGATTGAACGCACAGAAGGATGGTATCAATTTAGTTTGTCTCACAAAA
TTAAGATCGAATCCAGAAAACAATGTTGGTCTTTTAACAATGGCAAAAACTGTAGAAGTT
TTAGCTACTCTGACTAGTGATGTAGGACGAATTATGTCAAAGATGCATCTCGTTCAACCC
AACGGAAATATTAATTTAGTAACTGGAATTAGAATTGCTCATCTTGTTCTAAAACATCGT
CAAGGCAAGAATCATAAAATGCGTATTGTACTTTTTATTGGATCACCACTTGAAGTGGAT
AAAGCTGAAATGGAAAAATTAGCTAAGAAATTGAAGAAAGAAAAAGTTAATGTCGATATT
GTGAGCTTTGGTGACCATCAAAAAAATAATGATGTGCTTACTTCATTTATTAATACATTG
AATGGAAAAGATGGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAA
GAAGCATTAATTTCATCAGCAATCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGT
GGTGCAGGCTTTGAATTTGGTGTTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTA
AGAGTTTCAATGGAAGAACAGCCTGTTTCTACTATTGCACCAACATCTGACGAAGCTATG
CTTGAACGTGCACTCGCATTGTCGACTGAGACACCGAGTGACGAGGCTATGCCAGATTTT
GCTAACATGACTGAAGAGGAACAAATTGCTTTTGCTATGCAAATGTCAATGCAAGATGCA
CAGGAGCCTATAACACAACAAGCAAAACGTCCAAAAAAAGACGATACACCAATGGAAGTT
GATGAAGATTATAATGAAGTAATTACTGATCCAGCATTTCTCCAGAGTGTTTTAGAAAAT
CTTCCTGGTGTAGATCCGCAATCTGAGGCAATACGTGGTGCAGTTGACTCCTTAAATAAA
GACAAAAAGTCTGATAAAGATGGAAAAGGCAGCGGATCTAAATAA

>g12937.t19 Gene=g12937 Length=354
MVLESTMICLDNSDYQRNGDYLPTRLNAQKDGINLVCLTKLRSNPENNVGLLTMAKTVEV
LATLTSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFIGSPLEVD
KAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSVPRGSQLQ
EALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQPVSTIAPTSDEAM
LERALALSTETPSDEAMPDFANMTEEEQIAFAMQMSMQDAQEPITQQAKRPKKDDTPMEV
DEDYNEVITDPAFLQSVLENLPGVDPQSEAIRGAVDSLNKDKKSDKDGKGSGSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g12937.t19 Coils Coil Coil 117 137 -
10 g12937.t19 Gene3D G3DSA:3.40.50.410 - 3 186 8.6E-70
11 g12937.t19 Gene3D G3DSA:1.10.10.890 - 236 278 5.9E-17
18 g12937.t19 MobiDBLite mobidb-lite consensus disorder prediction 279 299 -
17 g12937.t19 MobiDBLite mobidb-lite consensus disorder prediction 321 354 -
19 g12937.t19 MobiDBLite mobidb-lite consensus disorder prediction 335 354 -
6 g12937.t19 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 9 227 6.0E-121
8 g12937.t19 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 9 227 6.0E-121
5 g12937.t19 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 236 349 6.0E-121
7 g12937.t19 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 236 349 6.0E-121
1 g12937.t19 Pfam PF13519 von Willebrand factor type A domain 6 113 1.9E-21
4 g12937.t19 Pfam PF02809 Ubiquitin interaction motif 212 227 0.0096
3 g12937.t19 Pfam PF02809 Ubiquitin interaction motif 236 250 0.028
2 g12937.t19 Pfam PF02809 Ubiquitin interaction motif 264 280 0.002
20 g12937.t19 ProSiteProfiles PS50234 VWFA domain profile. 5 188 9.725
21 g12937.t19 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 211 227 8.686
22 g12937.t19 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 264 283 10.363
16 g12937.t19 SMART SM00327 VWA_4 2 188 1.8E-4
15 g12937.t19 SMART SM00726 uim 211 230 0.64
13 g12937.t19 SMART SM00726 uim 236 255 0.84
14 g12937.t19 SMART SM00726 uim 264 283 0.025
9 g12937.t19 SUPERFAMILY SSF53300 vWA-like 4 177 1.1E-30

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

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