Gene loci information

Transcript annotation

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

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_3 g2573 g2573.t2 TTS g2573.t2 18811906 18811906
chr_3 g2573 g2573.t2 isoform g2573.t2 18812034 18813339
chr_3 g2573 g2573.t2 exon g2573.t2.exon1 18812034 18812776
chr_3 g2573 g2573.t2 cds g2573.t2.CDS1 18812034 18812776
chr_3 g2573 g2573.t2 exon g2573.t2.exon2 18812981 18813339
chr_3 g2573 g2573.t2 cds g2573.t2.CDS2 18812981 18813026
chr_3 g2573 g2573.t2 TSS g2573.t2 NA NA

Sequences

>g2573.t2 Gene=g2573 Length=1102
AATAATTGATAAAAATCCACAGAGATCTGGATTTCATATAAGTGATATACTTCAGTTAAA
TAGTGAAGCAAATGTAGAAAATTCAAAACCACGAACATCAATTGACTACTCAATTTATAA
TTATAACGACTATCAGTCACGCCACTATTATTCTCCTTATCCGCATCCACAAATTCTTCC
ATCAACTTTATCTACTTTCGAGAGTGATCTTCCATTTTACAATGCTGCATTCAATTCACA
ACCACCTTCTGTATACAATAGTAACGTTTATTTTGCATCAGACACAACAAGTAATAGTTT
TTCCGGAAATCAAATGAATCGTTATCTTGTAAATGATGCAAATAATAACAGCAGTTATGC
ATCATATTATGAGCAACAATATCATCACCATCATCATCATCACACATCTCATCAAAATAT
AATGCCACAAACGAGTCCTGATTCAACTAGTCCACTAGTTAACACTGATTCTTCCTATCT
CACGCTTCCTCAACCAAAAAGTTCATCATATAGTTCAAGTTCACCATCACATGAAATGAC
ATCAAAAGAAACAAAGTACACAACTTTAAGTTCAATTTCACCACAAACATCGACAACAGC
AAAAAATGAAAATTTCTCAACTCATTCCACAGATCTTGATGTAGGTGGAAATAATGATGA
TCATTTGAGTATGGATGAAAGTAGTGAAAGTATCGATGAAATGCATGATGGAGCAAGTGA
TAGTCAAACAACATCACAAAATTCAAGTGAGAAAAAGCGAAAACGTCGTGTGCTCTTCAC
AAAATCTCAAACATTTGAACTTGAGCGACGTTTTCGACAGCAACGATATTTATCAGCACC
TGAAAGAGAACATCTTGCATCACTTATTGGTCTTACACCAACGCAGGTGAAGATTTGGTT
TCAAAATCATCGCTACAAGACGAAACGAGCAAGTCATGAAAAGTCACCAGGCACATCTAA
TACATTTCCAACAAGACTTCCATCACCTAATGCTATAAAACGTGTTCATGTGCCTGTATT
GATTTCTGATGGAAAACCAGTTTTAAATGATAATTTAAATTTTAATCAATCGAGTGGAGG
TCAAAAGTGGTGGCAAGTCTAA

>g2573.t2 Gene=g2573 Length=262
MNRYLVNDANNNSSYASYYEQQYHHHHHHHTSHQNIMPQTSPDSTSPLVNTDSSYLTLPQ
PKSSSYSSSSPSHEMTSKETKYTTLSSISPQTSTTAKNENFSTHSTDLDVGGNNDDHLSM
DESSESIDEMHDGASDSQTTSQNSSEKKRKRRVLFTKSQTFELERRFRQQRYLSAPEREH
LASLIGLTPTQVKIWFQNHRYKTKRASHEKSPGTSNTFPTRLPSPNAIKRVHVPVLISDG
KPVLNDNLNFNQSSGGQKWWQV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2573.t2 CDD cd00086 homeodomain 149 205 1.00754E-20
10 g2573.t2 Gene3D G3DSA:1.10.10.60 - 112 210 5.1E-25
16 g2573.t2 MobiDBLite mobidb-lite consensus disorder prediction 22 152 -
14 g2573.t2 MobiDBLite mobidb-lite consensus disorder prediction 34 109 -
15 g2573.t2 MobiDBLite mobidb-lite consensus disorder prediction 110 132 -
2 g2573.t2 PANTHER PTHR24340:SF82 HOMEOBOX PROTEIN VND 16 246 7.0E-65
3 g2573.t2 PANTHER PTHR24340 HOMEOBOX PROTEIN NKX 16 246 7.0E-65
6 g2573.t2 PRINTS PR00024 Homeobox signature 170 181 8.7E-6
8 g2573.t2 PRINTS PR00031 Lambda-repressor HTH signature 177 186 4.0E-5
5 g2573.t2 PRINTS PR00024 Homeobox signature 185 195 8.7E-6
7 g2573.t2 PRINTS PR00031 Lambda-repressor HTH signature 186 202 4.0E-5
4 g2573.t2 PRINTS PR00024 Homeobox signature 195 204 8.7E-6
1 g2573.t2 Pfam PF00046 Homeodomain 149 205 6.7E-20
13 g2573.t2 ProSitePatterns PS00027 ‘Homeobox’ domain signature. 181 204 -
17 g2573.t2 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 146 206 20.018
12 g2573.t2 SMART SM00389 HOX_1 148 210 1.2E-23
9 g2573.t2 SUPERFAMILY SSF46689 Homeodomain-like 131 206 1.37E-24

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

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