Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Paired box protein Pax-6.

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 g8380 g8380.t2 isoform g8380.t2 30092871 30099725
chr_2 g8380 g8380.t2 exon g8380.t2.exon1 30092871 30092982
chr_2 g8380 g8380.t2 cds g8380.t2.CDS1 30092871 30092982
chr_2 g8380 g8380.t2 exon g8380.t2.exon2 30093049 30093220
chr_2 g8380 g8380.t2 cds g8380.t2.CDS2 30093049 30093220
chr_2 g8380 g8380.t2 exon g8380.t2.exon3 30098407 30098663
chr_2 g8380 g8380.t2 cds g8380.t2.CDS3 30098407 30098482
chr_2 g8380 g8380.t2 exon g8380.t2.exon4 30099342 30099725
chr_2 g8380 g8380.t2 TSS g8380.t2 30099718 30099718
chr_2 g8380 g8380.t2 TTS g8380.t2 NA NA

Sequences

>g8380.t2 Gene=g8380 Length=925
GTACGTTGCATTCGCTATTTGAGCTGTCGGATGTAACAGTCGCGATTTTGCCGAGACAAA
CAAATTTTTTAATTTTATTTCTGCACAAGTGATATCAAGCTCAAGTCGACGTTTGGATAC
GGATACACAAAGAACAAGCACAGAAAATTTTTTCTCTCATTGAAATCTTCGAAGAAAGTT
TTGTGAATAAATTTTGTTTTAATAAATTTCTTGTAATATATTCTCGACGGTAACACCTTT
CTTTCCATACATGGTTTTTATACCATGATAGACATTTAAATAAATTAGTTACATTAAGTT
CATCAATGTTAATACAATTCGGCAAGCGAGACGCGATAGACATAAAGAAATTTTAGTGTA
AAATACAGAAATAAAAAAAATATTTAACTTTTGCAATACTAAAATAATCATGCAATAATA
AAGTGCAACAATGAAATATTAAAATAAAGAAGGCGAAATATAAAAGAAACAATTTTTAGA
GACAAATAAAATTTTAGTTTTAAACGGGAAAAGACAAAAAGCCTTCAAAATTTTCGCGCT
ACAGAATTCTACGGCCCTGAATTCCATGGGCGCATCGCCCTGGTCTTCAACGATGATGAT
GGATCGCATATCACTCGATGATATGCCTCATAAAGGTAGAGCGTCTTCAGGATCGGGAGT
AAATCAATTAGGCGGAATCTTTGTAGGTGGCCGACCATTGCCGGACTCAACGAGACAGAA
GATTGTTGAACTGGCGCATTCGGGTGCTCGACCTTGCGATATATCTAGAATCTTGCAAGT
CTCCAATGGCTGCGTTAGCAAAATTTTAGGAAGATATTATGAAACTGGTAGTATAAGGCC
AAGAGCGATTGGCGGTTCAAAACCAAGAGTTGCAACAACTGAAGTTGTTAATAAAATTTC
ACACTACAAGCGTGAATGTCCTTCG

>g8380.t2 Gene=g8380 Length=120
MGASPWSSTMMMDRISLDDMPHKGRASSGSGVNQLGGIFVGGRPLPDSTRQKIVELAHSG
ARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATTEVVNKISHYKRECPS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g8380.t2 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 20 95 8.5E-41
9 g8380.t2 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 96 120 3.8E-8
2 g8380.t2 PANTHER PTHR45636:SF5 PAIRED BOX PROTEIN PAX-6-RELATED 18 120 1.5E-69
3 g8380.t2 PANTHER PTHR45636 PAIRED BOX PROTEIN PAX-6-RELATED-RELATED 18 120 1.5E-69
6 g8380.t2 PRINTS PR00027 Paired box signature 32 47 4.8E-43
7 g8380.t2 PRINTS PR00027 Paired box signature 50 68 4.8E-43
5 g8380.t2 PRINTS PR00027 Paired box signature 70 87 4.8E-43
4 g8380.t2 PRINTS PR00027 Paired box signature 88 105 4.8E-43
1 g8380.t2 Pfam PF00292 ‘Paired box’ domain 30 120 5.2E-50
11 g8380.t2 ProSitePatterns PS00034 Paired DNA-binding domain signature. 62 78 -
13 g8380.t2 ProSiteProfiles PS51057 Paired DNA-binding domain profile. 28 120 46.141
12 g8380.t2 SMART SM00351 pax3 28 120 4.1E-45
8 g8380.t2 SUPERFAMILY SSF46689 Homeodomain-like 31 119 1.82E-27

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
GO:0006355 regulation of transcription, DNA-templated BP

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. There were no conditions that were differentially expressed