Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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_2 g5926 g5926.t7 TTS g5926.t7 12878406 12878406
chr_2 g5926 g5926.t7 isoform g5926.t7 12879294 12881579
chr_2 g5926 g5926.t7 exon g5926.t7.exon1 12879294 12879653
chr_2 g5926 g5926.t7 cds g5926.t7.CDS1 12879296 12879653
chr_2 g5926 g5926.t7 exon g5926.t7.exon2 12879723 12880168
chr_2 g5926 g5926.t7 cds g5926.t7.CDS2 12879723 12880168
chr_2 g5926 g5926.t7 exon g5926.t7.exon3 12881454 12881579
chr_2 g5926 g5926.t7 cds g5926.t7.CDS3 12881454 12881579
chr_2 g5926 g5926.t7 TSS g5926.t7 12881780 12881780

Sequences

>g5926.t7 Gene=g5926 Length=932
ATGGACTCAGAAATGATTTTAAATCTCGTAATAAAAGTCCAGCAATTTGAGGACAAACGA
ATTGAGGCGAAAGCATCATGGAATATAAGAGAATTAAAAGGAAAACTTAGTGAAATATAT
CCTACAAGCACTGAAGAACAGAAACTTATATATTCTGGAAAGCTCTTGAACGATACTGTT
ATATTAAAGGACGTTTTACGAGAATACGAAGGACAAGAGGCTCATACAGTTCATTTAGTT
TTCACACCCAAACAAAATTCGCGTATTCAAAATAAATTTCAGGAAAGCAAACAAAATTCA
TCTGTCAACTCCATTAATAACCAGACATCATCATCGTCATCAGATATGAGTACAAGCGAA
TTAAGACAGAGACATACAGCTACTGCCACTGTTGCTCCTAACAATACAACTGAACAACAA
CAGATGACTTCTAGTAGCAACATTCCTAATAATTATTTTAATGCTTTCTATGGTAATACA
ATGGACGCTAATAATATTTTGGCTCAACAATATGCAATGCAAACATGGATGCAACAAGCT
TATGCTCAGTATATGAGTCAATATATGAATATTATGTCACAATCAGAGCAACAAGCTAAT
GCTCAAACAACAAATTTTGCTTTTATGCAGCCTCCAATGCCTTCTATACCAACTCCAACT
ACAGTGACTCCATCAACACAATCGCCAAATGCTGAAACTCAAGCAGCATCTGCAACTCCT
GTAGCGGAACAACAACAAGCACAACAGAATCAACCTGCAGCCGAGCCACAACGTCGATTT
CCAAACATCATTCAAGATGAGCAGGAAAATCGTGATTGGCTTGATATTCTTTATTCAATG
TCTCGTCTTATGATACTTTTGTGTCTTGTCTATTTTTATTCGTCGCCTCTTAGATGTCTC
ATTGTAATTCTCATAGGTGTATCAATTTATTT

>g5926.t7 Gene=g5926 Length=310
MDSEMILNLVIKVQQFEDKRIEAKASWNIRELKGKLSEIYPTSTEEQKLIYSGKLLNDTV
ILKDVLREYEGQEAHTVHLVFTPKQNSRIQNKFQESKQNSSVNSINNQTSSSSSDMSTSE
LRQRHTATATVAPNNTTEQQQMTSSSNIPNNYFNAFYGNTMDANNILAQQYAMQTWMQQA
YAQYMSQYMNIMSQSEQQANAQTTNFAFMQPPMPSIPTPTTVTPSTQSPNAETQAASATP
VAEQQQAQQNQPAAEPQRRFPNIIQDEQENRDWLDILYSMSRLMILLCLVYFYSSPLRCL
IVILIGVSIY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g5926.t7 Gene3D G3DSA:3.10.20.90 - 2 89 7.5E-17
11 g5926.t7 MobiDBLite mobidb-lite consensus disorder prediction 92 145 -
12 g5926.t7 MobiDBLite mobidb-lite consensus disorder prediction 219 264 -
13 g5926.t7 MobiDBLite mobidb-lite consensus disorder prediction 220 256 -
2 g5926.t7 PANTHER PTHR12943:SF27 HOMOCYSTEINE-INDUCED ENDOPLASMIC RETICULUM PROTEIN, ISOFORM A 9 310 2.4E-50
3 g5926.t7 PANTHER PTHR12943 HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM-RESIDENT UNIQUITIN-LIKE DOMAIN HERPUD PROTEIN FAMILY MEMBER 9 310 2.4E-50
1 g5926.t7 Pfam PF00240 Ubiquitin family 11 83 4.8E-10
6 g5926.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 282 -
8 g5926.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 283 309 -
7 g5926.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 310 310 -
14 g5926.t7 ProSiteProfiles PS50053 Ubiquitin domain profile. 7 86 14.164
10 g5926.t7 SMART SM00213 ubq_7 7 82 3.3E-8
4 g5926.t7 SUPERFAMILY SSF54236 Ubiquitin-like 7 85 5.76E-14
9 g5926.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 283 305 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5926/g5926.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5926.t7.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

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