Gene loci information

Transcript annotation

  • This transcript has been annotated as Homeobox protein extradenticle.

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 g13158 g13158.t9 TTS g13158.t9 28285238 28285238
chr_1 g13158 g13158.t9 isoform g13158.t9 28286048 28287831
chr_1 g13158 g13158.t9 exon g13158.t9.exon1 28286048 28286133
chr_1 g13158 g13158.t9 cds g13158.t9.CDS1 28286049 28286133
chr_1 g13158 g13158.t9 exon g13158.t9.exon2 28286220 28286409
chr_1 g13158 g13158.t9 cds g13158.t9.CDS2 28286220 28286409
chr_1 g13158 g13158.t9 exon g13158.t9.exon3 28286521 28286953
chr_1 g13158 g13158.t9 cds g13158.t9.CDS3 28286521 28286920
chr_1 g13158 g13158.t9 exon g13158.t9.exon4 28287770 28287831
chr_1 g13158 g13158.t9 TSS g13158.t9 28287918 28287918

Sequences

>g13158.t9 Gene=g13158 Length=771
TTTATATTATTTTGCGCAAAATAGTATTAAAGTGACACAAATCATAAAGAGTTCGTTAAA
AAGTGTCTAAAAGCAGCAACTTGCAGGCCGAATAAATGGAAGATCCAAATCGTATGATGG
CTCATGCAGCATCAAATCCTTCATACGCACAGCCATATGGTATGCCAAGTGATTCGCAAT
CGGTTGGTGATGACCCACGAAAGCAGGACATTGGTGAAATTCTTCAACAAATTATGAACA
TCACTGATCAATCACTTGATGAAGCACAAGCTCGAAAGCACACACTTAATTGTCATCGCA
TGAAGCCGGTTCTTTTTGCAGTGCTCTGTGAGATCAAGGAGAAAACAGTATTGTCATTAC
GCAATACTCAAGAGGAAGAACCTCCAGATCCTCAACTCATGCGTTTAGATAACATGCTTA
TTGCAGAAGGTGTTGCTGGTCCCGAAAAAGGCGGCGGTGCAGGAGCAGCAGCTTCTGCTT
CAGCGGCCGCATCAGATTTATTCCCCAAAGAGGACTTTGGTGACATGGGCAGTGGTCAGG
ACAATGCTATTGAGCATTCTGACTACCGCGCCAAATTGGCTCAAATTCGTCAAATTTATC
ATCAAGAACTCGAAAAATATGAACAAGCATGCAGTGAATTTACAACACACGTTATGAATC
TGCTACGTGAACAGAGTAGAACACGCCCCATTACACCGAAAGAAATTGAACGAATGGTAC
AGATTATTCACAAGAAATTCAGCTCGATTCAAATGCAGTTAAAACAATCTA

>g13158.t9 Gene=g13158 Length=225
MEDPNRMMAHAASNPSYAQPYGMPSDSQSVGDDPRKQDIGEILQQIMNITDQSLDEAQAR
KHTLNCHRMKPVLFAVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKGG
GAGAAASASAAASDLFPKEDFGDMGSGQDNAIEHSDYRAKLAQIRQIYHQELEKYEQACS
EFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g13158.t9 MobiDBLite mobidb-lite consensus disorder prediction 1 34 -
2 g13158.t9 PANTHER PTHR11850:SF50 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR 2 15 225 1.2E-109
3 g13158.t9 PANTHER PTHR11850 HOMEOBOX PROTEIN TRANSCRIPTION FACTORS 15 225 1.2E-109
1 g13158.t9 Pfam PF03792 PBC domain 36 225 1.1E-81

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005634 nucleus CC
GO:0003700 DNA-binding transcription factor activity 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