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.t16 TTS g12937.t16 27009496 27009496
chr_1 g12937 g12937.t16 isoform g12937.t16 27009648 27011251
chr_1 g12937 g12937.t16 exon g12937.t16.exon1 27009648 27009871
chr_1 g12937 g12937.t16 cds g12937.t16.CDS1 27009648 27009871
chr_1 g12937 g12937.t16 exon g12937.t16.exon2 27009934 27010018
chr_1 g12937 g12937.t16 cds g12937.t16.CDS2 27009934 27010018
chr_1 g12937 g12937.t16 exon g12937.t16.exon3 27010151 27010699
chr_1 g12937 g12937.t16 cds g12937.t16.CDS3 27010151 27010699
chr_1 g12937 g12937.t16 exon g12937.t16.exon4 27010752 27010866
chr_1 g12937 g12937.t16 cds g12937.t16.CDS4 27010752 27010866
chr_1 g12937 g12937.t16 exon g12937.t16.exon5 27010930 27011089
chr_1 g12937 g12937.t16 cds g12937.t16.CDS5 27010930 27011089
chr_1 g12937 g12937.t16 exon g12937.t16.exon6 27011239 27011251
chr_1 g12937 g12937.t16 cds g12937.t16.CDS6 27011239 27011251
chr_1 g12937 g12937.t16 TSS g12937.t16 27011325 27011325

Sequences

>g12937.t16 Gene=g12937 Length=1146
ATGGTTTTAGAAAAATTTCTTTGTCATTTTAGCTTGGATAATAGCGATTATCAACGTAAT
GGAGATTATCTACCAACAAGATTGAACGCACAGAAGGATGGTATCAATTTAGTTTGTCTC
ACAAAATTAAGATCGAATCCAGAAAACAATGTTGGTCTTTTAACAATGGCAAAAACTGTA
GAAGTTTTAGCTACTCTGACTAGTGATGTAGGACGAATTATGTCAAAGATGCATCTCGTT
CAACCCAACGGAAATATTAATTTAGTAACTGGAATTAGAATTGCTCATCTTGTTCTAAAA
CATCGTCAAGGCAAGAATCATAAAATGCGTATTGTACTTTTTATTGGATCACCACTTGAA
GTGGATAAAGCTGAAATGGAAAAATTAGCTAAGAAATTGAAGAAAGAAAAAGTTAATGTC
GATATTGTGAGCTTTGGTGACCATCAAAAAAATAATGATGTGCTTACTTCATTTATTAAT
ACATTGAATGGAAAAGATGGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAA
TTGCAAGAAGCATTAATTTCATCAGCAATCATTCAAGGAGAAGATGGAATGGGCGCAGGA
ATTGGTGGTGCAGGCTTTGAATTTGGTGTTGATCCTAATGAGGATCCAGAACTTGCTCTT
GCTTTAAGAGTTTCAATGGAAGAACAGCGTCAGCGACAAGAAGAAGAGCAAAGACGTGCA
CAAGCAGCTTCTGCTCAAGAAACTTCAACTGAAAATGCTCCAGCTGTTTCTACTATTGCA
CCAACATCTGACGAAGCTATGCTTGAACGTGCACTCGCATTGTCGACTGAGACACCGAGT
GACGAGGCTATGCCAGATTTTGCTAACATGACTGAAGAGGAACAAATTGCTTTTGCTATG
CAAATGTCAATGCAAGATGCACAGGAGCCTATAACACAACAAGCAAAACGTCCAAAAAAA
GACGATACACCAATGGAAGTTGATGAAGATTATAATGAAGTAATTACTGATCCAGCATTT
CTCCAGAGTGTTTTAGAAAATCTTCCTGGTGTAGATCCGCAATCTGAGGCAATACGTGGT
GCAGTTGACTCCTTAAATAAAGACAAAAAGTCTGATAAAGATGGAAAAGGCAGCGGATCT
AAATAA

>g12937.t16 Gene=g12937 Length=381
MVLEKFLCHFSLDNSDYQRNGDYLPTRLNAQKDGINLVCLTKLRSNPENNVGLLTMAKTV
EVLATLTSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFIGSPLE
VDKAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSVPRGSQ
LQEALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEEEQRRA
QAASAQETSTENAPAVSTIAPTSDEAMLERALALSTETPSDEAMPDFANMTEEEQIAFAM
QMSMQDAQEPITQQAKRPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQSEAIRG
AVDSLNKDKKSDKDGKGSGSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12937.t16 Coils Coil Coil 119 139 -
11 g12937.t16 Coils Coil Coil 223 246 -
8 g12937.t16 Gene3D G3DSA:3.40.50.410 - 8 188 2.5E-65
9 g12937.t16 Gene3D G3DSA:1.10.10.890 - 263 305 6.5E-17
17 g12937.t16 MobiDBLite mobidb-lite consensus disorder prediction 226 263 -
16 g12937.t16 MobiDBLite mobidb-lite consensus disorder prediction 227 241 -
19 g12937.t16 MobiDBLite mobidb-lite consensus disorder prediction 242 259 -
21 g12937.t16 MobiDBLite mobidb-lite consensus disorder prediction 307 327 -
18 g12937.t16 MobiDBLite mobidb-lite consensus disorder prediction 345 381 -
20 g12937.t16 MobiDBLite mobidb-lite consensus disorder prediction 362 381 -
5 g12937.t16 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 10 376 3.6E-137
6 g12937.t16 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 10 376 3.6E-137
1 g12937.t16 Pfam PF13519 von Willebrand factor type A domain 11 115 1.4E-19
4 g12937.t16 Pfam PF02809 Ubiquitin interaction motif 214 229 0.01
2 g12937.t16 Pfam PF02809 Ubiquitin interaction motif 263 277 0.031
3 g12937.t16 Pfam PF02809 Ubiquitin interaction motif 291 307 0.0022
22 g12937.t16 ProSiteProfiles PS50234 VWFA domain profile. 10 190 9.02
24 g12937.t16 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 213 232 10.732
23 g12937.t16 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 291 310 10.363
15 g12937.t16 SMART SM00327 VWA_4 5 190 5.7E-4
14 g12937.t16 SMART SM00726 uim 213 232 0.021
12 g12937.t16 SMART SM00726 uim 263 282 0.84
13 g12937.t16 SMART SM00726 uim 291 310 0.025
7 g12937.t16 SUPERFAMILY SSF53300 vWA-like 11 179 1.49E-27

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.

Raw TPM values