Gene loci information

Transcript annotation

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

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 g4236 g4236.t1 TTS g4236.t1 522684 522684
chr_2 g4236 g4236.t1 isoform g4236.t1 523363 530460
chr_2 g4236 g4236.t1 exon g4236.t1.exon1 523363 523774
chr_2 g4236 g4236.t1 cds g4236.t1.CDS1 523363 523774
chr_2 g4236 g4236.t1 exon g4236.t1.exon2 530210 530460
chr_2 g4236 g4236.t1 cds g4236.t1.CDS2 530210 530460
chr_2 g4236 g4236.t1 TSS g4236.t1 NA NA

Sequences

>g4236.t1 Gene=g4236 Length=663
ATGGGCATATCAGAAGACACGAAGTTAGAGGAGATACCTCGTGAGGGCAGATCACCACAG
GACAATCGTTCGAGTGCAACAACAAGTTTTGGTGGTCACAGTCCTATGTCAGATCATAGC
GATGTTGATCTTGATAATGAGTATCCACAAAAACGGAAACAGCGACGCTATCGAACGACA
TTCACAAGTTATCAACTTGAAGAACTAGAGAAGGCCTTCTCTCGTACACATTATCCAGAT
GTTTTTACTAGTGTTGGTGGACTTTATTCGCCTGCTAGTGCATCATTTCAGACACTTCTA
GCCAATATTTCAGCTGCTCAACGACCACCACCAATTCTTCCAACAATGCCTACCAAATCT
TCTTCTGAATATATACCTGTAAGCTTAGCTTTGACTGTATCACCACCAATTTCTCCAACT
GATTCCAATAAGTCATCAACTTCAGCACCATTGACACCAATTAATGCTTCATCACCTACT
GCTGCTGCTGCTGCTGCATCACATCAAAGTGCATTATCACCAAATGCAAACACCACCAGC
TCAACACCACCACCTGAAGATCGTCGTAGCTCATCTATTGCTGCATTACGTTTAAAAGCA
CGTGAACATGAAATGCGTCTCGAAATGATGCGTCAAAATGGACATGATGTGTTAAGCAAT
TAA

>g4236.t1 Gene=g4236 Length=220
MGISEDTKLEEIPREGRSPQDNRSSATTSFGGHSPMSDHSDVDLDNEYPQKRKQRRYRTT
FTSYQLEELEKAFSRTHYPDVFTSVGGLYSPASASFQTLLANISAAQRPPPILPTMPTKS
SSEYIPVSLALTVSPPISPTDSNKSSTSAPLTPINASSPTAAAAAASHQSALSPNANTTS
STPPPEDRRSSSIAALRLKAREHEMRLEMMRQNGHDVLSN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4236.t1 CDD cd00086 homeodomain 55 83 3.61779E-7
9 g4236.t1 Coils Coil Coil 193 213 -
8 g4236.t1 Gene3D G3DSA:1.10.10.60 - 40 86 2.8E-12
12 g4236.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 61 -
16 g4236.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 18 -
15 g4236.t1 MobiDBLite mobidb-lite consensus disorder prediction 19 35 -
14 g4236.t1 MobiDBLite mobidb-lite consensus disorder prediction 38 54 -
11 g4236.t1 MobiDBLite mobidb-lite consensus disorder prediction 157 188 -
13 g4236.t1 MobiDBLite mobidb-lite consensus disorder prediction 157 193 -
4 g4236.t1 PANTHER PTHR24329:SF548 HOMEOBOX PROTEIN ARX 46 83 2.0E-27
6 g4236.t1 PANTHER PTHR24329 HOMEOBOX PROTEIN ARISTALESS 46 83 2.0E-27
3 g4236.t1 PANTHER PTHR24329:SF548 HOMEOBOX PROTEIN ARX 147 207 2.0E-27
5 g4236.t1 PANTHER PTHR24329 HOMEOBOX PROTEIN ARISTALESS 147 207 2.0E-27
2 g4236.t1 Pfam PF00046 Homeodomain 55 81 1.5E-6
1 g4236.t1 Pfam PF03826 OAR motif 187 204 5.5E-9
17 g4236.t1 ProSiteProfiles PS50803 OAR domain profile. 191 204 11.859
7 g4236.t1 SUPERFAMILY SSF46689 Homeodomain-like 32 82 7.45E-10

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

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