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.t2 TTS g13158.t2 28283894 28283894
chr_1 g13158 g13158.t2 isoform g13158.t2 28284075 28286133
chr_1 g13158 g13158.t2 exon g13158.t2.exon1 28284075 28285963
chr_1 g13158 g13158.t2 cds g13158.t2.CDS1 28285525 28285963
chr_1 g13158 g13158.t2 exon g13158.t2.exon2 28286023 28286133
chr_1 g13158 g13158.t2 cds g13158.t2.CDS2 28286023 28286105
chr_1 g13158 g13158.t2 TSS g13158.t2 28286129 28286129

Sequences

>g13158.t2 Gene=g13158 Length=2000
CCCCATTACACCGAAAGAAATTGAACGAATGGTACAGATTATTCACAAGAAATTCAGCTC
GATTCAAATGCAGTTAAAACAATCTACTTGCGAAGCTGTCATGATTTTGAGATCACGATT
TTTGGATGCTCGTCGCAAGCGAAGAAACTTTAGTAAACAAGCTTCCGAAATTCTCAATGA
ATATTTCTATAGCCACCTTAGCAATCCTTATCCATCAGAAGAGGCAAAAGAGGATTTAGC
TCGAAAATGTGGCATCACTGTCTCTCAAGTATCCAACTGGTTTGGAAATAAACGCATTCG
TTACAAGAAGAATATTGGCAAAGCACAGGAGGAAGCAAATCTTTATGCAGCAAAGAAGGC
AGCTGGTGCCAGTCCATATTCTATGGCAGGCCCTCCTTCAGGTGCTACAACACCAATGAT
GAGTCCAGCACCTGCACAAGATTCAATGGGATATTCACTCGGATCAGGTGGTTACGATCA
ACAGCAAGCATATGATGGCAGTATGGGTGGATACGATATGCATCAAGGTAAAGATCGTGA
TGACTTTTGAGTCGATAACACATAAATTTATGTGCAAAAAAAATTACAGCAACAATTAAA
TGAAGAAACCACTAATAATTTTAACTTATACAAGAATTTTTAATTTTTTTTATTACATGT
TAGTCTTTGAGAAACAAGATTAATATGTTTGTAATAGAAATCCACTTTAAGTTAGAGAAA
TTGCAAAATTAGTTGTAAAATTTATTTTTATTATCGTTCATCTCCTTTTATTATTACGAA
TATAGGCATCAAACATTTTTTTTATTTCAATACCATATAAAAACTTAAATATATCAGAGA
AAGAAGAAAAACCACTTTAGCATTAATTTAAAGAATATTTTACACCAAGAAACAAGAAAC
ATAAAATTTGCATCAAACTATTTTCATTTACCCCTTTTTGCATAGAATTAAGCTCTCAAG
ACGCACAAATATCTTTGTGTGATCAACAAAAAATTCGCTTTTAGCTTTTATTTCTCTGCA
ACAAGGCACAAAAATTAGTAAATGAGTATACAAAAAAAAATTATTGAGAAATTAAAAGAT
TTTTTTCTCATGATTTATGTTCAATGAAGAGAAAAAGAAGTTAATAAATCTATACGATCA
ATTTTTTGAATAATAATGTACCATAATGATATACGAAGCAATTATACGAACATTTGGGTT
TGAGCAAATTTTTTTAAAATTCTTTCCCAATACGAAAAGAATAATATATTTGAATTACAA
ACCAACACACATTTGAATTTTGATCAAATTGATATACGTAAAAATTTTTAAAGAAGAAAT
TTCTTTATCTAATTTCTTTTCTGCCTATTAAAAATGTATGAGAGACTCTCAATAGTAATG
AAGTCTCTGATCTATTGTGTTTTTATTCAAAATTGAAGTAACAAGTATACGAAAACTAAA
AACAGTTACGTTTTAAAAACAATGAGATATAAGTAGTGTTTTTTGCCGAATTGCCACCAA
CATAAGTCACACAATTCTTTCATGATGAGTGATTGTAAGAAAATGGCATAATTTTTTTCT
TTGATTCTGTTGTCACAATGATTTATCTTCATTTCTTCTTTTGTTTCTAAAGATGTGCAA
AATTTGCTAAATAATAATAGTAAAATAATCATAAGAATATATCAAATGTCTGATGATGAA
TTGCTTTGTGAAATGAGAGTATAAACGAATTAAATTAATTTCAGCAATGCTTTTTCTTAG
AAAATTAAACTTTTTAGACTTTAAGGATTATTATGATGATAACAATTTAAGAAAAAACAG
TAAACAAGATTTTTAACATTTCCTTCCTTCCTTTCCTTTTTTCACTAAACTCTCTCACTC
TTTCTTTTCTTCTGTCATTATACAGAGTACAGTACACAAATTAATAAAACAATAGATCAT
AATAAATATTTCGCAATAAATAAATGGGAAAATTTTCTTGTGAAATAAATACCTACCTAA
ATGAACTTATAAAATGAGAA

>g13158.t2 Gene=g13158 Length=173
MVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNP
YPSEEAKEDLARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMA
GPPSGATTPMMSPAPAQDSMGYSLGSGGYDQQQAYDGSMGGYDMHQGKDRDDF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13158.t2 CDD cd00086 homeodomain 35 95 1.82131E-19
6 g13158.t2 Gene3D G3DSA:1.10.10.60 - 33 108 3.7E-32
11 g13158.t2 MobiDBLite mobidb-lite consensus disorder prediction 124 147 -
10 g13158.t2 MobiDBLite mobidb-lite consensus disorder prediction 154 173 -
3 g13158.t2 PANTHER PTHR11850:SF108 HOMEOBOX PROTEIN EXTRADENTICLE 1 133 1.8E-78
4 g13158.t2 PANTHER PTHR11850 HOMEOBOX PROTEIN TRANSCRIPTION FACTORS 1 133 1.8E-78
1 g13158.t2 Pfam PF03792 PBC domain 1 33 2.2E-13
2 g13158.t2 Pfam PF00046 Homeodomain 35 94 3.0E-19
8 g13158.t2 ProSitePatterns PS00027 ‘Homeobox’ domain signature. 70 93 -
12 g13158.t2 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 32 95 17.07
9 g13158.t2 SMART SM00389 HOX_1 34 99 3.4E-17
5 g13158.t2 SUPERFAMILY SSF46689 Homeodomain-like 34 102 1.28E-20

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:0003677 DNA binding MF
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific MF
GO:0006355 regulation of transcription, DNA-templated BP
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