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.t4 TTS g13158.t4 28285238 28285238
chr_1 g13158 g13158.t4 isoform g13158.t4 28285525 28286920
chr_1 g13158 g13158.t4 exon g13158.t4.exon1 28285525 28285963
chr_1 g13158 g13158.t4 cds g13158.t4.CDS1 28285525 28285963
chr_1 g13158 g13158.t4 exon g13158.t4.exon2 28286023 28286133
chr_1 g13158 g13158.t4 cds g13158.t4.CDS2 28286023 28286133
chr_1 g13158 g13158.t4 exon g13158.t4.exon3 28286220 28286409
chr_1 g13158 g13158.t4 cds g13158.t4.CDS3 28286220 28286409
chr_1 g13158 g13158.t4 exon g13158.t4.exon4 28286521 28286920
chr_1 g13158 g13158.t4 cds g13158.t4.CDS4 28286521 28286920
chr_1 g13158 g13158.t4 TSS g13158.t4 28287918 28287918

Sequences

>g13158.t4 Gene=g13158 Length=1140
ATGGAAGATCCAAATCGTATGATGGCTCATGCAGCATCAAATCCTTCATACGCACAGCCA
TATGGTATGCCAAGTGATTCGCAATCGGTTGGTGATGACCCACGAAAGCAGGACATTGGT
GAAATTCTTCAACAAATTATGAACATCACTGATCAATCACTTGATGAAGCACAAGCTCGA
AAGCACACACTTAATTGTCATCGCATGAAGCCGGTTCTTTTTGCAGTGCTCTGTGAGATC
AAGGAGAAAACAGTATTGTCATTACGCAATACTCAAGAGGAAGAACCTCCAGATCCTCAA
CTCATGCGTTTAGATAACATGCTTATTGCAGAAGGTGTTGCTGGTCCCGAAAAAGGCGGC
GGTGCAGGAGCAGCAGCTTCTGCTTCAGCGGCCGCATCAGATTTATTCCCCAAAGAGGAC
TTTGGTGACATGGGCAGTGGTCAGGACAATGCTATTGAGCATTCTGACTACCGCGCCAAA
TTGGCTCAAATTCGTCAAATTTATCATCAAGAACTCGAAAAATATGAACAAGCATGCAGT
GAATTTACAACACACGTTATGAATCTGCTACGTGAACAGAGTAGAACACGCCCCATTACA
CCGAAAGAAATTGAACGAATGGTACAGATTATTCACAAGAAATTCAGCTCGATTCAAATG
CAGTTAAAACAATCTACTTGCGAAGCTGTCATGATTTTGAGATCACGATTTTTGGATGCT
CGTCGCAAGCGAAGAAACTTTAGTAAACAAGCTTCCGAAATTCTCAATGAATATTTCTAT
AGCCACCTTAGCAATCCTTATCCATCAGAAGAGGCAAAAGAGGATTTAGCTCGAAAATGT
GGCATCACTGTCTCTCAAGTATCCAACTGGTTTGGAAATAAACGCATTCGTTACAAGAAG
AATATTGGCAAAGCACAGGAGGAAGCAAATCTTTATGCAGCAAAGAAGGCAGCTGGTGCC
AGTCCATATTCTATGGCAGGCCCTCCTTCAGGTGCTACAACACCAATGATGAGTCCAGCA
CCTGCACAAGATTCAATGGGATATTCACTCGGATCAGGTGGTTACGATCAACAGCAAGCA
TATGATGGCAGTATGGGTGGATACGATATGCATCAAGGTAAAGATCGTGATGACTTTTGA

>g13158.t4 Gene=g13158 Length=379
MEDPNRMMAHAASNPSYAQPYGMPSDSQSVGDDPRKQDIGEILQQIMNITDQSLDEAQAR
KHTLNCHRMKPVLFAVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKGG
GAGAAASASAAASDLFPKEDFGDMGSGQDNAIEHSDYRAKLAQIRQIYHQELEKYEQACS
EFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDA
RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEDLARKCGITVSQVSNWFGNKRIRYKK
NIGKAQEEANLYAAKKAAGASPYSMAGPPSGATTPMMSPAPAQDSMGYSLGSGGYDQQQA
YDGSMGGYDMHQGKDRDDF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13158.t4 CDD cd00086 homeodomain 241 301 1.19072E-17
7 g13158.t4 Coils Coil Coil 376 379 -
6 g13158.t4 Gene3D G3DSA:1.10.10.60 - 239 314 1.7E-31
11 g13158.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 34 -
12 g13158.t4 MobiDBLite mobidb-lite consensus disorder prediction 360 379 -
3 g13158.t4 PANTHER PTHR11850:SF50 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR 2 15 327 1.5E-177
4 g13158.t4 PANTHER PTHR11850 HOMEOBOX PROTEIN TRANSCRIPTION FACTORS 15 327 1.5E-177
1 g13158.t4 Pfam PF03792 PBC domain 36 239 5.8E-92
2 g13158.t4 Pfam PF00046 Homeodomain 241 300 1.2E-18
10 g13158.t4 ProSitePatterns PS00027 ‘Homeobox’ domain signature. 276 299 -
13 g13158.t4 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 238 301 17.07
9 g13158.t4 SMART SM00389 HOX_1 240 305 3.4E-17
5 g13158.t4 SUPERFAMILY SSF46689 Homeodomain-like 240 308 5.99E-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

Pathway

  • This transcript belongs to the following pathways

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