Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA-binding protein D-ETS-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 g5885 g5885.t1 TTS g5885.t1 12586494 12586494
chr_2 g5885 g5885.t1 isoform g5885.t1 12586568 12592556
chr_2 g5885 g5885.t1 exon g5885.t1.exon1 12586568 12586886
chr_2 g5885 g5885.t1 cds g5885.t1.CDS1 12586568 12586886
chr_2 g5885 g5885.t1 exon g5885.t1.exon2 12586943 12586954
chr_2 g5885 g5885.t1 cds g5885.t1.CDS2 12586943 12586954
chr_2 g5885 g5885.t1 exon g5885.t1.exon3 12587023 12587067
chr_2 g5885 g5885.t1 cds g5885.t1.CDS3 12587023 12587067
chr_2 g5885 g5885.t1 exon g5885.t1.exon4 12587120 12587228
chr_2 g5885 g5885.t1 cds g5885.t1.CDS4 12587120 12587228
chr_2 g5885 g5885.t1 exon g5885.t1.exon5 12587363 12587488
chr_2 g5885 g5885.t1 cds g5885.t1.CDS5 12587363 12587488
chr_2 g5885 g5885.t1 exon g5885.t1.exon6 12592133 12592556
chr_2 g5885 g5885.t1 cds g5885.t1.CDS6 12592133 12592556
chr_2 g5885 g5885.t1 TSS g5885.t1 12592869 12592869

Sequences

>g5885.t1 Gene=g5885 Length=1035
ATGCAAAGAAATGACAGTGAAATAGTGATAAACGATGATGATAGTGAAAGTACAAGCATT
GAATCTCTTTTAGTGCAAAAATATGAGTCACCATCAAATAGTGGTGGCAGTGAGGTTGTT
GAAAGTAGTGCGCAGGATGAGAATGATGAAGTCATTTTTGTGCCAAATAATCCGACAACA
TGGTCGGAAAAGCATATTGAAACATGGGTTAAATGGGCATCAGATCAATTTGAAATTAAA
CCGCCATTGGATGTTTCGCGCTTTCCAAAAAGTGGTGCAGAATTGGCAAAATTTACTAAA
GCAGATTTCTTTATCATCTGCGGATCATTCGAGGGCGGTAGAATGGTTATGGATCATTTT
AAATATATGATGGAAAATGTTGGTGAAAGTGTCGAAGAAACGCTCCTTACTGATGGTGAA
CCAGATCCGTATCAACTTTTAAATGCCACGTCGCGTTTGGTTAATTCGGGATCTGGGCAG
ATACAATTATGGCAATTTTTGTTAGAGCTTCTCGCTGATTCGTCGAATTCTGATTTTATA
AAGTGGGAGGGAACTGCTGGTGAATTTAAATTAATCGATCCAGATGAGGTGGCGAGACGA
TGGGGTGTTAAGAAAAATAAAACAAATATGAATTATGATAAACTAAGTCGTGCATTGAGA
TATTATTATGATAAATCAATCATGACGAAAGTACATGGAAAAAGGTACGCTTATAGGTTT
GACTTTCATGGATTAATGGCAGCTTGTCATGCACAAGCACAAGGATGTGATTCAACAAGT
ATGCTTCCAAAATACCCTCCACATCTCCTTATGCCAAATGATTTTTCAAGTTATGCAAGC
ACATCGACTGCCATTCCTACAAGTACAAATCAAGTATCAGCAGCATTGTCATCATCTTTC
AAACCAGTACAACCAATCATTACTCCTCATGCAACTCCTTCTACTTCTTCATCATCGTCA
TCACCATCGACAGTGGCACAAACACCAAACACTGAAAGAATACCTGGATGGCCATATTTA
CCCTCAAACTTTTAA

>g5885.t1 Gene=g5885 Length=344
MQRNDSEIVINDDDSESTSIESLLVQKYESPSNSGGSEVVESSAQDENDEVIFVPNNPTT
WSEKHIETWVKWASDQFEIKPPLDVSRFPKSGAELAKFTKADFFIICGSFEGGRMVMDHF
KYMMENVGESVEETLLTDGEPDPYQLLNATSRLVNSGSGQIQLWQFLLELLADSSNSDFI
KWEGTAGEFKLIDPDEVARRWGVKKNKTNMNYDKLSRALRYYYDKSIMTKVHGKRYAYRF
DFHGLMAACHAQAQGCDSTSMLPKYPPHLLMPNDFSSYASTSTAIPTSTNQVSAALSSSF
KPVQPIITPHATPSTSSSSSSPSTVAQTPNTERIPGWPYLPSNF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5885.t1 Gene3D G3DSA:1.10.150.50 Transcription Factor 34 126 2.5E-15
11 g5885.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 127 256 8.7E-47
17 g5885.t1 MobiDBLite mobidb-lite consensus disorder prediction 29 48 -
18 g5885.t1 MobiDBLite mobidb-lite consensus disorder prediction 310 332 -
19 g5885.t1 MobiDBLite mobidb-lite consensus disorder prediction 310 331 -
3 g5885.t1 PANTHER PTHR11849 ETS 26 342 1.5E-93
4 g5885.t1 PANTHER PTHR11849:SF295 DNA-BINDING PROTEIN D-ETS-6-LIKE PROTEIN 26 342 1.5E-93
7 g5885.t1 PRINTS PR00454 ETS domain signature 161 174 8.2E-30
5 g5885.t1 PRINTS PR00454 ETS domain signature 185 203 8.2E-30
6 g5885.t1 PRINTS PR00454 ETS domain signature 204 222 8.2E-30
8 g5885.t1 PRINTS PR00454 ETS domain signature 223 241 8.2E-30
1 g5885.t1 Pfam PF02198 Sterile alpha motif (SAM)/Pointed domain 52 123 2.1E-10
2 g5885.t1 Pfam PF00178 Ets-domain 162 240 6.0E-34
13 g5885.t1 ProSitePatterns PS00345 Ets-domain signature 1. 163 171 -
14 g5885.t1 ProSitePatterns PS00346 Ets-domain signature 2. 207 222 -
20 g5885.t1 ProSiteProfiles PS51433 Pointed (PNT) domain profile. 40 127 27.047
21 g5885.t1 ProSiteProfiles PS50061 Ets-domain profile. 161 241 44.964
15 g5885.t1 SMART SM00251 SAM2_3 41 127 0.0089
16 g5885.t1 SMART SM00413 etsneu2 160 245 1.5E-55
9 g5885.t1 SUPERFAMILY SSF47769 SAM/Pointed domain 43 123 1.79E-14
10 g5885.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 158 289 4.63E-48

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5885/g5885.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5885.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006355 regulation of transcription, DNA-templated BP
GO:0043565 sequence-specific DNA binding MF
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.

Raw TPM values