General information for g5885.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA-binding protein D-ETS-6.
Parent gene
- The parent gene g5885 is located on chr_2: 12592133..12592869 (- strand)
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.t6 | isoform | g5885.t6 | 12585866 | 12592556 |
| chr_2 | g5885 | g5885.t6 | exon | g5885.t6.exon1 | 12585866 | 12586886 |
| chr_2 | g5885 | g5885.t6 | exon | g5885.t6.exon2 | 12587016 | 12587067 |
| chr_2 | g5885 | g5885.t6 | exon | g5885.t6.exon3 | 12587120 | 12587217 |
| chr_2 | g5885 | g5885.t6 | cds | g5885.t6.CDS1 | 12587210 | 12587217 |
| chr_2 | g5885 | g5885.t6 | exon | g5885.t6.exon4 | 12587363 | 12587488 |
| chr_2 | g5885 | g5885.t6 | cds | g5885.t6.CDS2 | 12587363 | 12587488 |
| chr_2 | g5885 | g5885.t6 | exon | g5885.t6.exon5 | 12592133 | 12592556 |
| chr_2 | g5885 | g5885.t6 | cds | g5885.t6.CDS3 | 12592133 | 12592556 |
| chr_2 | g5885 | g5885.t6 | TSS | g5885.t6 | 12592869 | 12592869 |
| chr_2 | g5885 | g5885.t6 | TTS | g5885.t6 | NA | NA |
Sequences
>g5885.t6 Gene=g5885 Length=1721
ATGCAAAGAAATGACAGTGAAATAGTGATAAACGATGATGATAGTGAAAGTACAAGCATT
GAATCTCTTTTAGTGCAAAAATATGAGTCACCATCAAATAGTGGTGGCAGTGAGGTTGTT
GAAAGTAGTGCGCAGGATGAGAATGATGAAGTCATTTTTGTGCCAAATAATCCGACAACA
TGGTCGGAAAAGCATATTGAAACATGGGTTAAATGGGCATCAGATCAATTTGAAATTAAA
CCGCCATTGGATGTTTCGCGCTTTCCAAAAAGTGGTGCAGAATTGGCAAAATTTACTAAA
GCAGATTTCTTTATCATCTGCGGATCATTCGAGGGCGGTAGAATGGTTATGGATCATTTT
AAATATATGATGGAAAATGTTGGTGAAAGTGTCGAAGAAACGCTCCTTACTGATGGTGAA
CCAGATCCGTATCAACTTTTAAATGCCACGTCGCGTTTGGTTAATTCGGGATCTGGGCAG
ATACAATTATGGCAATTTTTGTTAGAGCTTCTCGCTGATTCGTCGAATTCTGATTTTATA
AAGTGGGAGGGAATTTAAATTAATCGATCCAGATGAGGTGGCGAGACGATGGGGTGTTAA
GAAAAATAAAACAAATATGAATTATGATAAACTAAGTCGTGCATTGAGATATTATTATGA
TAAATCAATCATGACGAAAGTACATGGAAAAAGGTGAGAAGTTTGACTTTCATGGATTAA
TGGCAGCTTGTCATGCACAAGCACAAGGATGTGATTCAACAAGTATGCTTCCAAAATACC
CTCCACATCTCCTTATGCCAAATGATTTTTCAAGTTATGCAAGCACATCGACTGCCATTC
CTACAAGTACAAATCAAGTATCAGCAGCATTGTCATCATCTTTCAAACCAGTACAACCAA
TCATTACTCCTCATGCAACTCCTTCTACTTCTTCATCATCGTCATCACCATCGACAGTGG
CACAAACACCAAACACTGAAAGAATACCTGGATGGCCATATTTACCCTCAAACTTTTAAA
CAATTGAAATCTCAAATAATTTGTAAATGACATCGTTTTAATTGTCAGCATATAAAAGGC
TATTCTGATCTCAAATTGTGAATTTATTATTATTTTTCCTTTAATTTCAGTCCCTTTTCC
TTTTCTATTGTTTCAATTTTCTGTTCTTTCCTCCAGTGAATTACATTTTTTTATACAAAC
ATCACATGAATAATTTTTATACGTAAGTCTGTGTAGCAATAATTAAAACTTTTTTTAATT
TTAAAAATACATTCTTAATGAAGATATTGATACCTCAGCTGTTAGATAATAAGAAGAACA
ATTTAAATTTAAATCAAATGCTCAAAACTATAAAAAAAGTTCATGTGACAAATCTCTTTA
TGTCTCTTCTTTTAGTGTTGAGAATATGAAAGAATGTTGTAATTAGATAATAAGTAGATG
TTTTTTGTAATTATTCAAATCCTAATCAAATTATCTTAATATAATGATTAGAAATAAATC
AGTGAATTAATAAAAGAACATGTTTAAAAGAAATATGCATTTTTATGCGAAACGTTTTCA
GAATCGGTAAAATGAGAAACGCTACTCAAATAAAACATGTTGTGCAACATTTTCTTCCCT
CTTTTTTGTTACGTCTCATAGAGTCTCATAAACATACTTTGTGCATGACACATTTAACTG
AAATTTTACAACGGTAAAGAAGAAAACTATTGAATATTATT
>g5885.t6 Gene=g5885 Length=185
MQRNDSEIVINDDDSESTSIESLLVQKYESPSNSGGSEVVESSAQDENDEVIFVPNNPTT
WSEKHIETWVKWASDQFEIKPPLDVSRFPKSGAELAKFTKADFFIICGSFEGGRMVMDHF
KYMMENVGESVEETLLTDGEPDPYQLLNATSRLVNSGSGQIQLWQFLLELLADSSNSDFI
KWEGI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5885.t6 | Gene3D | G3DSA:1.10.150.50 | Transcription Factor | 34 | 125 | 6.8E-16 |
| 6 | g5885.t6 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 126 | 185 | 1.4E-9 |
| 10 | g5885.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 28 | 48 | - |
| 11 | g5885.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 28 | 42 | - |
| 2 | g5885.t6 | PANTHER | PTHR11849 | ETS | 25 | 184 | 9.5E-29 |
| 3 | g5885.t6 | PANTHER | PTHR11849:SF295 | DNA-BINDING PROTEIN D-ETS-6-LIKE PROTEIN | 25 | 184 | 9.5E-29 |
| 1 | g5885.t6 | Pfam | PF02198 | Sterile alpha motif (SAM)/Pointed domain | 52 | 123 | 6.1E-11 |
| 8 | g5885.t6 | ProSitePatterns | PS00345 | Ets-domain signature 1. | 163 | 171 | - |
| 12 | g5885.t6 | ProSiteProfiles | PS51433 | Pointed (PNT) domain profile. | 40 | 127 | 27.047 |
| 13 | g5885.t6 | ProSiteProfiles | PS50061 | Ets-domain profile. | 161 | 185 | 13.366 |
| 9 | g5885.t6 | SMART | SM00251 | SAM2_3 | 41 | 127 | 0.0089 |
| 4 | g5885.t6 | SUPERFAMILY | SSF47769 | SAM/Pointed domain | 42 | 123 | 4.49E-15 |
| 5 | g5885.t6 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 158 | 184 | 2.55E-6 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5885/g5885.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5885.t6.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
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