Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Homeobox protein MOX-1.

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 g507 g507.t1 isoform g507.t1 3820360 3821470
chr_3 g507 g507.t1 exon g507.t1.exon1 3820360 3820607
chr_3 g507 g507.t1 cds g507.t1.CDS1 3820360 3820607
chr_3 g507 g507.t1 exon g507.t1.exon2 3820891 3821470
chr_3 g507 g507.t1 cds g507.t1.CDS2 3820891 3821470
chr_3 g507 g507.t1 TSS g507.t1 NA NA
chr_3 g507 g507.t1 TTS g507.t1 NA NA

Sequences

>g507.t1 Gene=g507 Length=828
ATGTATACGCCAAATGTGAATAAAAGTAGTGAAACATATTTTGAGCATTGCGTACCATCA
ATGTTTTCAAATAAAATGACAAATCAATCGATTCAGTCAAATTATTTTAGTGATCATCAA
TCAGAATTCAGTCAGCAAACACCTTTAAATATTTATAATAATTATAATCCAAATTTTCAT
CACCATCACTATTATTATCCTAATTATGATTATGCATACCAAAATTCTTCACTAGAACAA
AATTGGGTTAGAAAATATGATTGTGAGAACCAAAAAGAATATTTTATTGCAAATACACCA
CCAACTCCTTCAGATTATTGTGATTTTGAAGTTCCTCAACAGCAGTTTGATTCAAACAAA
TCAACAGTTCGTTGTGATGTTGAAAAATTTTATTGTGACACGTACAAATCAGCAAAAAAT
CAAATTAATAATAATTTCATTGAACCATGTGAAAATTTTGGTGGATATTGGAATGGTGAT
AAAAATTCTAAAAAGTGCATGAAAATTGAGGAGAAATTAGTCAAAAGTGAAAATTCAAAG
AAGGATAAAAATATAAAGAGAATGAAACATACTGATTTTGACGATCAAATTTCTTCACCG
TCATCTTTAATTTCAAATCGAAAAGAAAGAACAGCATTTACAAAGGAGCAAGTCAAAAAC
CTTGAATTCGAATTTTCAAACTCAAATTATTTGACAAGATTAAGGAGATATGAAATAGCT
GTTGCATTGGGTTTATCTGAAAGACAAGTAAAAGTTTGGTTTCAAAATCGTCGAATGAAG
CATAAGAGATCTGTAAAAGGAGTTGATGCATCAAGTGAAACAGAATAA

>g507.t1 Gene=g507 Length=275
MYTPNVNKSSETYFEHCVPSMFSNKMTNQSIQSNYFSDHQSEFSQQTPLNIYNNYNPNFH
HHHYYYPNYDYAYQNSSLEQNWVRKYDCENQKEYFIANTPPTPSDYCDFEVPQQQFDSNK
STVRCDVEKFYCDTYKSAKNQINNNFIEPCENFGGYWNGDKNSKKCMKIEEKLVKSENSK
KDKNIKRMKHTDFDDQISSPSSLISNRKERTAFTKEQVKNLEFEFSNSNYLTRLRRYEIA
VALGLSERQVKVWFQNRRMKHKRSVKGVDASSETE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g507.t1 CDD cd00086 homeodomain 207 264 1.20488E-19
9 g507.t1 Gene3D G3DSA:1.10.10.60 - 159 267 2.5E-24
2 g507.t1 PANTHER PTHR24328 HOMEOBOX PROTEIN MOX 59 268 7.4E-32
4 g507.t1 PRINTS PR00024 Homeobox signature 228 239 7.3E-7
6 g507.t1 PRINTS PR00031 Lambda-repressor HTH signature 235 244 2.8E-6
3 g507.t1 PRINTS PR00024 Homeobox signature 243 253 7.3E-7
7 g507.t1 PRINTS PR00031 Lambda-repressor HTH signature 244 260 2.8E-6
5 g507.t1 PRINTS PR00024 Homeobox signature 253 262 7.3E-7
1 g507.t1 Pfam PF00046 Homeodomain 207 263 5.5E-21
11 g507.t1 ProSitePatterns PS00027 ‘Homeobox’ domain signature. 239 262 -
13 g507.t1 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 204 264 20.99
12 g507.t1 SMART SM00389 HOX_1 206 268 2.3E-23
8 g507.t1 SUPERFAMILY SSF46689 Homeodomain-like 193 263 1.41E-23

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g507/g507.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g507.t1.fa.iupred3.txt does not exist

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:0045944 positive regulation of transcription by RNA polymerase II BP
GO:0006355 regulation of transcription, DNA-templated BP
GO:0003700 DNA-binding transcription factor activity 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