Gene loci information

Transcript annotation

  • This transcript has been annotated as Longitudinals lacking protein-like.

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 g5836 g5836.t5 TSS g5836.t5 12213210 12213210
chr_2 g5836 g5836.t5 isoform g5836.t5 12213234 12215321
chr_2 g5836 g5836.t5 exon g5836.t5.exon1 12213234 12213238
chr_2 g5836 g5836.t5 exon g5836.t5.exon2 12214073 12214244
chr_2 g5836 g5836.t5 cds g5836.t5.CDS1 12214149 12214244
chr_2 g5836 g5836.t5 exon g5836.t5.exon3 12214335 12214409
chr_2 g5836 g5836.t5 cds g5836.t5.CDS2 12214335 12214409
chr_2 g5836 g5836.t5 exon g5836.t5.exon4 12214478 12214566
chr_2 g5836 g5836.t5 cds g5836.t5.CDS3 12214478 12214566
chr_2 g5836 g5836.t5 exon g5836.t5.exon5 12214635 12215321
chr_2 g5836 g5836.t5 cds g5836.t5.CDS4 12214635 12214758
chr_2 g5836 g5836.t5 TTS g5836.t5 12215662 12215662

Sequences

>g5836.t5 Gene=g5836 Length=1028
GCTAATAAACGGGCATCATCAAACCATAATAAAAACAACAAATAACAAAACTACCAACAG
AGTGAAAATCGTCATATAAAGATGGGCGAGCAGCAATTTTTCTTGAAATGGAATGACTTT
CAAAACAACATGGTCTCATCATTCAAACACTTGCGTGATGAAAAAAGCTTTACCGATGTG
ACTCTAGCATGTGATGGCCAAACTTGCAAAGCACACAAAATGGTTCTATCTGCCTGCAGT
CCATATTTCAAGACTTTGCTTGAAGAAAATCCATCAAAACATCCGATTATCATTTTGAAG
GATGTTTCATTCAATCATTTGCAAGCTATCTTAGAATTCATGTATGCAGGAGAAGTTAAT
GTTTCGCAGGAACAATTGCCCTCATTCTTGAAAACAGCTGATAGATTAAAAGTAAAAGGC
CTTGCAGAGACTCAATCACCGTTCTCAAACAAGAGAGAGGGTTGATAAGTTAATCGTTGT
CATCATCATCTTTTCTCGACCCCTCCGAGCATAAGATATTAAAATCTCATTAAAAACGCT
CTTCATTTCCTTCCTCCTTCTTTCTTTTTTTTCAAACTCCTTTCCTATCTTTTATCTGAT
ACAATTGATACATTCGATATAATTCTTGAAAAATTCTCTTTTCACTTTAAATTTTGTTTT
GTAGATTAATTCAATATTTTACTTTTATTTTTGATTCTTTAATAATCCCTTTGCCCTTTG
AAGCGTAGAAAGATAATAGGAGTTAGATAATACACATACAACACAGACATTCTATAAAGA
GACGTTTTTAAGAAAAAGAAAATTTAATAATTTAGTTCTTCCTTTTTTGATTTCACTTTT
CTTTAAATTAGTGTCCCTCGCAAGAATTATAAAAAGAAAATTTTAAAATTAATGAGTACT
TCTTTTCAATTTCATCTTTAAAAAGCTTTTCTTCATTTTTAACTCAGTTTCTTATTCACT
AAATTTTTTTGGCACTCATGATTGTGCTCGACTGAGTGAGGACTTTAAAATTTAAAAAAT
TTTCTCTA

>g5836.t5 Gene=g5836 Length=127
MGEQQFFLKWNDFQNNMVSSFKHLRDEKSFTDVTLACDGQTCKAHKMVLSACSPYFKTLL
EENPSKHPIIILKDVSFNHLQAILEFMYAGEVNVSQEQLPSFLKTADRLKVKGLAETQSP
FSNKREG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5836.t5 CDD cd18315 BTB_POZ_BAB-like 30 113 0.00
6 g5836.t5 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 4 119 0.00
2 g5836.t5 PANTHER PTHR23110:SF95 LONGITUDINALS LACKING PROTEIN-LIKE-RELATED 2 118 0.00
3 g5836.t5 PANTHER PTHR23110 BTB DOMAIN TRANSCRIPTION FACTOR 2 118 0.00
1 g5836.t5 Pfam PF00651 BTB/POZ domain 21 117 0.00
7 g5836.t5 ProSiteProfiles PS50097 BTB domain profile. 31 96 22.65
5 g5836.t5 SMART SM00225 BTB_4 31 126 0.00
4 g5836.t5 SUPERFAMILY SSF54695 POZ domain 7 116 0.00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5836/g5836.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5836.t5.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