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_3 g560 g560.t2 TTS g560.t2 4051144 4051144
chr_3 g560 g560.t2 isoform g560.t2 4051404 4052474
chr_3 g560 g560.t2 exon g560.t2.exon1 4051404 4051412
chr_3 g560 g560.t2 cds g560.t2.CDS1 4051404 4051412
chr_3 g560 g560.t2 exon g560.t2.exon2 4051467 4051581
chr_3 g560 g560.t2 cds g560.t2.CDS2 4051467 4051581
chr_3 g560 g560.t2 exon g560.t2.exon3 4051640 4052100
chr_3 g560 g560.t2 cds g560.t2.CDS3 4051640 4052100
chr_3 g560 g560.t2 exon g560.t2.exon4 4052159 4052474
chr_3 g560 g560.t2 cds g560.t2.CDS4 4052159 4052410
chr_3 g560 g560.t2 TSS g560.t2 NA NA

Sequences

>g560.t2 Gene=g560 Length=901
TGATTTGACGTTGGAAAACACGTTTGGTTTGAGAGTTTATATTTGTGCAAAATTAATTAA
AAACATGAACACAACTGATCTCTGTGAATGCAATATACTTGATAAGTTCGAATGTTGCGA
ATGCGATGAATGTTACACATATAAATTTACAAAACACAAATGCTACATCAAATTGAACAA
TGAATTATATGAACTTATATTCGACGATATGTGTGACGAGCCTGAATTTGATGAAGACGA
ACCGATTGAACATACATGGTGTCTTTATGATGATGATCTGAAGCTTGATGACGATGTGCT
TGTGATTGATCTTCATCTAAATTTCAATTATAAAATAATGCAATGCATTCAATCACATCC
ATATGAAGATTATCTTGGTGATAAGAATTTCAATGAGCTAAAAATTATTTGTTCTGATGG
CATTATACTTTATGCAAACCGATTAATTTTGGCTATGAATTCTTCTGTTTTTAGAACAAT
GTTTCAGACAAATATGATTGAGAGCGAAATGAAAGAAGTTGTTGTAAACGACATTGATTC
AAAAACTATGCAAGAATTTTTACGCTTTGCTTATAGTAGCAAAATTGAAAATTTAGATTA
TGTTGCTGAATCATTATTATACTGTGCTGAAAAATACGAAGTAAATGATCTCAAGAATAC
ATGCATCGCACATCTTATCAAGAATTTGAAGAAGGATAATGTTTTTGAAATTTTGCAACT
GGCTGAAATGCTAAACTTGAAAATAATGATGAATCAATGTTTGAATTTTATCTGCAAATC
ATTTGAAAAAGTAGAAGATGTCAATGAATTCGATAGATTGAATGAAAGTTTGAAAAAGAA
AGTAATTGAAGGAAAATGTAAAATGTTTATCGAGCCCATTACAACTTATGTTCCTAAATG
A

>g560.t2 Gene=g560 Length=278
MNTTDLCECNILDKFECCECDECYTYKFTKHKCYIKLNNELYELIFDDMCDEPEFDEDEP
IEHTWCLYDDDLKLDDDVLVIDLHLNFNYKIMQCIQSHPYEDYLGDKNFNELKIICSDGI
ILYANRLILAMNSSVFRTMFQTNMIESEMKEVVVNDIDSKTMQEFLRFAYSSKIENLDYV
AESLLYCAEKYEVNDLKNTCIAHLIKNLKKDNVFEILQLAEMLNLKIMMNQCLNFICKSF
EKVEDVNEFDRLNESLKKKVIEGKCKMFIEPITTYVPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g560.t2 CDD cd18186 BTB_POZ_ZBTB_KLHL-like 114 191 0.000e+00
8 g560.t2 CDD cd14733 BACK 211 262 1.350e-05
6 g560.t2 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 98 245 0.000e+00
2 g560.t2 PANTHER PTHR24413:SF213 FI01029P-RELATED 26 248 0.000e+00
3 g560.t2 PANTHER PTHR24413 SPECKLE-TYPE POZ PROTEIN 26 248 0.000e+00
1 g560.t2 Pfam PF00651 BTB/POZ domain 107 207 0.000e+00
7 g560.t2 ProSiteProfiles PS50097 BTB domain profile. 110 178 1.537e+01
5 g560.t2 SMART SM00225 BTB_4 110 208 0.000e+00
4 g560.t2 SUPERFAMILY SSF54695 POZ domain 101 206 0.000e+00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g560/g560.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g560.t2.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. There were no conditions that were differentially expressed