Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Homeobox protein orthopedia.

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 g7582 g7582.t2 TSS g7582.t2 24679429 24679429
chr_2 g7582 g7582.t2 isoform g7582.t2 24680078 24697006
chr_2 g7582 g7582.t2 exon g7582.t2.exon1 24680078 24680111
chr_2 g7582 g7582.t2 cds g7582.t2.CDS1 24680078 24680111
chr_2 g7582 g7582.t2 exon g7582.t2.exon2 24685235 24685428
chr_2 g7582 g7582.t2 cds g7582.t2.CDS2 24685235 24685428
chr_2 g7582 g7582.t2 exon g7582.t2.exon3 24685504 24685603
chr_2 g7582 g7582.t2 cds g7582.t2.CDS3 24685504 24685603
chr_2 g7582 g7582.t2 exon g7582.t2.exon4 24685933 24685991
chr_2 g7582 g7582.t2 cds g7582.t2.CDS4 24685933 24685991
chr_2 g7582 g7582.t2 exon g7582.t2.exon5 24696911 24696922
chr_2 g7582 g7582.t2 cds g7582.t2.CDS5 24696911 24696922
chr_2 g7582 g7582.t2 exon g7582.t2.exon6 24696986 24697006
chr_2 g7582 g7582.t2 cds g7582.t2.CDS6 24696986 24697006
chr_2 g7582 g7582.t2 TTS g7582.t2 NA NA

Sequences

>g7582.t2 Gene=g7582 Length=420
ATGCTGAATAATCTCAGCACATCAGTGATTGGAGACTTATTTTTTAATGGCATTTCAGGA
AGCCAAAACCAAAAAGATTGTGATTTACCTAAAACGACTGTCTTGCATGGATCAAATAGC
TTTGGTCAATTGCAAAGTCCAACAACGAACGTATCTGACACAACAAACAACACACGATTG
CATGTTTCGAGCGGACTCTGTGACTCGCACAGCATGCATCAAGATCAAAATAATGATAAA
AATGCAAAACAGAAACGACATAGAACACGATTCACGCCAGCACAGCTGAATGAGCTCGAA
AGGTGCTTCGGAAAGACACACTATCCAGATATTTTTATGCGTGAGGAGATTGCTATGAGA
ATTGGATTAACAGAATCAAGAGTACAAGTTTGGTTCCAAAATTTTATTAACTGTGATTAA

>g7582.t2 Gene=g7582 Length=139
MLNNLSTSVIGDLFFNGISGSQNQKDCDLPKTTVLHGSNSFGQLQSPTTNVSDTTNNTRL
HVSSGLCDSHSMHQDQNNDKNAKQKRHRTRFTPAQLNELERCFGKTHYPDIFMREEIAMR
IGLTESRVQVWFQNFINCD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7582.t2 CDD cd00086 homeodomain 85 134 0.000
5 g7582.t2 Gene3D G3DSA:1.10.10.60 - 68 135 0.000
2 g7582.t2 PANTHER PTHR46770 HOMEOBOX PROTEIN ORTHOPEDIA 63 134 0.000
1 g7582.t2 Pfam PF00046 Homeodomain 85 134 0.000
6 g7582.t2 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 82 134 16.244
4 g7582.t2 SMART SM00389 HOX_1 84 138 0.000
3 g7582.t2 SUPERFAMILY SSF46689 Homeodomain-like 67 134 0.000

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:0003677 DNA binding MF

KEGG

Orthology

Pathway

This gene does not belong to any 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. There were no conditions that were differentially expressed