General information for g5548.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ets DNA-binding protein pokkuri.
Parent gene
- The parent gene g5548 is located on chr_2: 10215652..10217802 (- 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 | g5548 | g5548.t1 | TTS | g5548.t1 | 10215046 | 10215046 |
| chr_2 | g5548 | g5548.t1 | isoform | g5548.t1 | 10215652 | 10217802 |
| chr_2 | g5548 | g5548.t1 | exon | g5548.t1.exon1 | 10215652 | 10215859 |
| chr_2 | g5548 | g5548.t1 | cds | g5548.t1.CDS1 | 10215652 | 10215859 |
| chr_2 | g5548 | g5548.t1 | exon | g5548.t1.exon2 | 10215924 | 10216295 |
| chr_2 | g5548 | g5548.t1 | cds | g5548.t1.CDS2 | 10215924 | 10216295 |
| chr_2 | g5548 | g5548.t1 | exon | g5548.t1.exon3 | 10216361 | 10216479 |
| chr_2 | g5548 | g5548.t1 | cds | g5548.t1.CDS3 | 10216361 | 10216479 |
| chr_2 | g5548 | g5548.t1 | exon | g5548.t1.exon4 | 10216539 | 10216669 |
| chr_2 | g5548 | g5548.t1 | cds | g5548.t1.CDS4 | 10216539 | 10216669 |
| chr_2 | g5548 | g5548.t1 | exon | g5548.t1.exon5 | 10216728 | 10217802 |
| chr_2 | g5548 | g5548.t1 | cds | g5548.t1.CDS5 | 10216728 | 10217802 |
| chr_2 | g5548 | g5548.t1 | TSS | g5548.t1 | 10218069 | 10218069 |
Sequences
>g5548.t1 Gene=g5548 Length=1905
ATGAAATTATTGCCAATTCCTTTATCGCCATTGGGAGCACCGCCCTTAAGCATGTGGAGT
TCTGACTTTCTCTGGCGTTATCCAGCTGCACCGCCAAGTCCTTTGGCTGAGTTAAAAACT
CAGCTGCCTACTCAACTTTCATCAGATCCTCGCCTATGGGGACGTGAAGAAGTTGTTGTC
TTTTTACGTTGGACAGAACGTGAATTTGATTTGCCCAAGTTTGAGCTTGATTTGTTTCAA
ATGAATGGAAAAGCACTTTGTTTATTAACAAAAAATGATTTAGCTGAACGATGCCCTGGA
GCTGGTGACATTATTCACAATGTCTTACAATTGCTCATTCGTGATGCACAGATGCTTCAA
AGACCATTTAGATCAGATTTGCCGAGCAGTCCTATTACACCAACAAATCGCTATCCACTT
TCACCGCACAGTCATCCACCGACTCCTAATTGGAATTCACTTGTGCCACCAAATGGTGAA
AATAGTTTTTATGCATCGCATTTGCAACATTTTATGACATCGAATTCAGTCACATTGAGT
CCTGCACCGTCAATTGATTCTCAAGCAGGTAGTCCACCTGGTCAAGAACCGCCTGCAAAT
ATATTCTCATCGAATAGTACAAATGATGTCGCTCAAGCTAGTACAAGTGATGCATCTGAT
GCTCGATCAAGTAGTGCCAGTGGAGCATCAGCAACAGCTGGAAACAGTTCACGAAGCAGC
AGCAATCACAGTGATTCCGAAGATGAAAGTGCAAATTTTAAGCACAAAATTCCAAAATTG
CTTCCACCACCAATTCATCATAAATCACTGTCAAATTCACTTCAAAAACATCAACAAAGT
CCACCAGTTACACCAATTTTTAAAGAATCTTCATCATCATCGACTACACCATCGCATCTT
ACACATCAAATTGGAGATTTTAAGCAGCACAGTATTTTTTTTAATGGCGCTCTTGATGCT
GTCACAAATACAAGTGGATCAAGTAGCAGTGCAAGCCCATCAACACCAACAACTCCAGGA
TATTTGTCAGTTAAAAGAGAATTCTTTCCTGATACACCAACTGAACCTAATACAAATGGT
CGATTACTTTGGGATTTTCTTCAGCAACTTCTTAATGATCATCAACAACGTTATAGCAAT
TATATTGCATGGAAATGTCGTGATACTGGAGTTTTTAAAATAGTTGATCCAGCTGGACTT
GCAAAACTTTGGGGAATTCAAAAGAATCATTTATCAATGAATTATGATAAGATGTCACGT
GCATTACGTTATTATTATCGTGTGAATATTCTACGTAAAGTGCAAGGAGAACGCCATTGT
TATCAATTTTTGCGAAATCCAACTGAATTGAAGAGCATAAAGAACATTTCACTGCTTCGT
CAAACGATGACAAATCAGCAACAACAACAACAATCGACAGCAACTGCATCATCAACAACT
TCATCATCGTCAGCAGAAGCGCAAAATTCTGCTGCTGCTGCCGCCTTGCAAGCATCCGCA
CTGGCAAGTTTATTACCACAGAGTACAACAAACTTTCATCATTTAACAGCAGCACTAGTA
CAAAGTAGCAATAATTTAAAGCTACAGTTCAGTGGTCGTAATGCAGAAGATGAACCTCAT
GATTTGAGTACATCATCATCAAATCAAAATGAAAGCTTTATAAAAAATGAAAGCTTTATA
AAAAATGAATGTTATCCACTCATTCATGGAGCAAATGGCTTAACGACCATTCAACTGTTA
CGTCAAAGCCAGGAAAATTCATCCTCACAATCACCATCATCATCGCCTACTTCATTGTCA
CCTCCCATCCATCATTTGTCGTTGCATAAAGAAAATCAAGAACAACATCAGCAGCAGCAA
CATGTTGAAGAAATGCCAACGGACTTAAGAAAAATTAATAATTGA
>g5548.t1 Gene=g5548 Length=634
MKLLPIPLSPLGAPPLSMWSSDFLWRYPAAPPSPLAELKTQLPTQLSSDPRLWGREEVVV
FLRWTEREFDLPKFELDLFQMNGKALCLLTKNDLAERCPGAGDIIHNVLQLLIRDAQMLQ
RPFRSDLPSSPITPTNRYPLSPHSHPPTPNWNSLVPPNGENSFYASHLQHFMTSNSVTLS
PAPSIDSQAGSPPGQEPPANIFSSNSTNDVAQASTSDASDARSSSASGASATAGNSSRSS
SNHSDSEDESANFKHKIPKLLPPPIHHKSLSNSLQKHQQSPPVTPIFKESSSSSTTPSHL
THQIGDFKQHSIFFNGALDAVTNTSGSSSSASPSTPTTPGYLSVKREFFPDTPTEPNTNG
RLLWDFLQQLLNDHQQRYSNYIAWKCRDTGVFKIVDPAGLAKLWGIQKNHLSMNYDKMSR
ALRYYYRVNILRKVQGERHCYQFLRNPTELKSIKNISLLRQTMTNQQQQQQSTATASSTT
SSSSAEAQNSAAAAALQASALASLLPQSTTNFHHLTAALVQSSNNLKLQFSGRNAEDEPH
DLSTSSSNQNESFIKNESFIKNECYPLIHGANGLTTIQLLRQSQENSSSQSPSSSPTSLS
PPIHHLSLHKENQEQHQQQQHVEEMPTDLRKINN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5548.t1 | Coils | Coil | Coil | 629 | 634 | - |
| 12 | g5548.t1 | Gene3D | G3DSA:1.10.150.50 | Transcription Factor | 41 | 124 | 3.9E-29 |
| 11 | g5548.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 345 | 466 | 6.1E-36 |
| 19 | g5548.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 207 | 241 | - |
| 23 | g5548.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 207 | 253 | - |
| 21 | g5548.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 270 | 300 | - |
| 18 | g5548.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 462 | 486 | - |
| 20 | g5548.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 582 | 602 | - |
| 24 | g5548.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 582 | 634 | - |
| 22 | g5548.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 607 | 634 | - |
| 3 | g5548.t1 | PANTHER | PTHR11849 | ETS | 18 | 554 | 1.9E-129 |
| 4 | g5548.t1 | PANTHER | PTHR11849:SF201 | ETS DNA-BINDING PROTEIN POKKURI | 18 | 554 | 1.9E-129 |
| 6 | g5548.t1 | PRINTS | PR00454 | ETS domain signature | 361 | 374 | 5.1E-20 |
| 8 | g5548.t1 | PRINTS | PR00454 | ETS domain signature | 388 | 406 | 5.1E-20 |
| 5 | g5548.t1 | PRINTS | PR00454 | ETS domain signature | 407 | 425 | 5.1E-20 |
| 7 | g5548.t1 | PRINTS | PR00454 | ETS domain signature | 426 | 444 | 5.1E-20 |
| 1 | g5548.t1 | Pfam | PF02198 | Sterile alpha motif (SAM)/Pointed domain | 40 | 114 | 4.9E-20 |
| 2 | g5548.t1 | Pfam | PF00178 | Ets-domain | 363 | 443 | 5.1E-30 |
| 16 | g5548.t1 | ProSitePatterns | PS00345 | Ets-domain signature 1. | 363 | 371 | - |
| 17 | g5548.t1 | ProSitePatterns | PS00346 | Ets-domain signature 2. | 410 | 425 | - |
| 25 | g5548.t1 | ProSiteProfiles | PS51433 | Pointed (PNT) domain profile. | 32 | 116 | 39.183 |
| 26 | g5548.t1 | ProSiteProfiles | PS50061 | Ets-domain profile. | 361 | 444 | 23.723 |
| 14 | g5548.t1 | SMART | SM00251 | SAM2_3 | 30 | 116 | 6.0E-24 |
| 15 | g5548.t1 | SMART | SM00413 | etsneu2 | 360 | 448 | 2.6E-50 |
| 9 | g5548.t1 | SUPERFAMILY | SSF47769 | SAM/Pointed domain | 13 | 116 | 8.85E-22 |
| 10 | g5548.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 359 | 492 | 2.69E-42 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5548/g5548.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5548.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0045892 | negative regulation of transcription, DNA-templated | BP |
| GO:0001709 | cell fate determination | BP |
| GO:0000122 | negative regulation of transcription by RNA polymerase II | BP |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0045596 | negative regulation of cell differentiation | BP |
| GO:0043565 | sequence-specific DNA binding | MF |
| GO:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03211 (ETS translocation variant 6/7)
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.
