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 g5347 g5347.t3 TTS g5347.t3 9067654 9067654
chr_2 g5347 g5347.t3 isoform g5347.t3 9068179 9069330
chr_2 g5347 g5347.t3 exon g5347.t3.exon1 9068179 9068891
chr_2 g5347 g5347.t3 cds g5347.t3.CDS1 9068179 9068891
chr_2 g5347 g5347.t3 exon g5347.t3.exon2 9068943 9069214
chr_2 g5347 g5347.t3 cds g5347.t3.CDS2 9068943 9069214
chr_2 g5347 g5347.t3 exon g5347.t3.exon3 9069282 9069330
chr_2 g5347 g5347.t3 cds g5347.t3.CDS3 9069282 9069292
chr_2 g5347 g5347.t3 TSS g5347.t3 9069401 9069401

Sequences

>g5347.t3 Gene=g5347 Length=1034
ATGGTTCAATATATTAAATGCATTTACAATAATAAAGAATGGAATATTCTGGTGCACATG
GAAAAGACAAATCCAATCAAGATGTCGATTCTATTTTATTCCAAAATTGCAAGTTTCAAA
GATTTCCACGAGGTCTTATTCAAGTTTTCCCGAATTTGAAATACCTTAATATATCATTCT
CTCAACTTACGTATATCGAGCGCAATGATTTAAAGGAATATGCACAACTTACTGATCTAT
ATTTGCATAAAAATCAACTTGTATATTTATCAGAAGACTTATTTGCAGACATGCCAAATT
TGGAAGTAATTTGGCTTCAAAATAATAATAATTTGCTTATCGAACCTAAAATTTTCAATA
ATTTGGTTCATTTAAAAAACTTAAGTCTCTCCAATCAATTCTATTTCAACATACTTCCAT
CTGCTAATCGAGGAAAAATGTCTCTTAATAGAATCAAATATGAATTACAAAAAATATATG
AAAATTCACCAATGAAGAAATTTTTGGAAGCAAAATTAAAGAACGAATTTTTCGATGATA
TCAAGAATGCAATTCGCAATGATGATCTAAAGGATTTCACAATAAATGTTCGAACTCGCC
AGTTTAAAGGACATAAGTTTATTCTTGCCTCTCGCAGTCAAGTTTTTGCTGAAATATTTA
AGAATAACAAAGATGCTGATAATCTAAAACTTAATAATGTATCTCCAGAAGTCTTTCAAA
TTGTTTTTGATTTCATTTATACAAACGAATTACCAAATTTAGATGAAGACACACTTGTAC
AAATTATAACGATCAGCGAACAACTAAAGATTAAGATATTAACAAAGCATGTTGAAGAAG
AACTTTTGATGATGGTCAACACTGAAAATGTTTCAAAAATGTTGAAACTGAGTGAAAAAT
TTAATTTGAAAAAACTAAAGCAGAAAAGTACAAGTGACAGAGAACAAGTCAGAATGCTAA
ACGAAGATACTGAAAAAATGCAGAAGGAATTGATGGCTATCAAGAAAATGCTAGAAAAGA
AAGAAAAAAAATGA

>g5347.t3 Gene=g5347 Length=331
MEYSGAHGKDKSNQDVDSILFQNCKFQRFPRGLIQVFPNLKYLNISFSQLTYIERNDLKE
YAQLTDLYLHKNQLVYLSEDLFADMPNLEVIWLQNNNNLLIEPKIFNNLVHLKNLSLSNQ
FYFNILPSANRGKMSLNRIKYELQKIYENSPMKKFLEAKLKNEFFDDIKNAIRNDDLKDF
TINVRTRQFKGHKFILASRSQVFAEIFKNNKDADNLKLNNVSPEVFQIVFDFIYTNELPN
LDEDTLVQIITISEQLKIKILTKHVEEELLMMVNTENVSKMLKLSEKFNLKKLKQKSTSD
REQVRMLNEDTEKMQKELMAIKKMLEKKEKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5347.t3 CDD cd18186 BTB_POZ_ZBTB_KLHL-like 179 256 1.41489E-19
8 g5347.t3 Coils Coil Coil 290 331 -
6 g5347.t3 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 7 149 9.2E-18
7 g5347.t3 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 150 299 3.2E-29
3 g5347.t3 PANTHER PTHR24410 HL07962P-RELATED 165 306 6.7E-20
1 g5347.t3 Pfam PF13855 Leucine rich repeat 63 119 4.5E-7
2 g5347.t3 Pfam PF00651 BTB/POZ domain 174 269 2.9E-20
11 g5347.t3 ProSiteProfiles PS50097 BTB domain profile. 178 242 15.783
10 g5347.t3 SMART SM00225 BTB_4 178 273 2.0E-18
4 g5347.t3 SUPERFAMILY SSF52058 L domain-like 18 129 4.16E-19
5 g5347.t3 SUPERFAMILY SSF54695 POZ domain 162 269 9.81E-21

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5347/g5347.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5347.t3.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

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.

Raw TPM values