General information for g15872.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA topoisomerase 2-binding protein 1-A.
Parent gene
- The parent gene g15872 is located on chr_4: 7133955..7135336 (+ 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_4 | g15872 | g15872.t1 | TSS | g15872.t1 | 7131034 | 7131034 |
| chr_4 | g15872 | g15872.t1 | isoform | g15872.t1 | 7131050 | 7135336 |
| chr_4 | g15872 | g15872.t1 | exon | g15872.t1.exon1 | 7131050 | 7131175 |
| chr_4 | g15872 | g15872.t1 | cds | g15872.t1.CDS1 | 7131050 | 7131175 |
| chr_4 | g15872 | g15872.t1 | exon | g15872.t1.exon2 | 7131578 | 7131753 |
| chr_4 | g15872 | g15872.t1 | cds | g15872.t1.CDS2 | 7131578 | 7131753 |
| chr_4 | g15872 | g15872.t1 | exon | g15872.t1.exon3 | 7132079 | 7134689 |
| chr_4 | g15872 | g15872.t1 | cds | g15872.t1.CDS3 | 7132079 | 7134689 |
| chr_4 | g15872 | g15872.t1 | exon | g15872.t1.exon4 | 7134755 | 7135336 |
| chr_4 | g15872 | g15872.t1 | cds | g15872.t1.CDS4 | 7134755 | 7135336 |
| chr_4 | g15872 | g15872.t1 | TTS | g15872.t1 | 7135369 | 7135369 |
Sequences
>g15872.t1 Gene=g15872 Length=3495
ATGGAGCAGTCAATATACAATAAACAATTTGATTTAACTAATCAAATATTTTCTGAAGAT
AACATTTGCTATGTTTATTTCGTTAAACATGAGAAAAATTCAAAAGATTTCATGGAGGAC
TTTCAAAAATTCAAAGATTTTCATGACCAAAAAAATGATTCAATAATTGAACTGATAGAT
GAAGAAAGATGTTTGAAATTCACAAAAGAAGAAATTGGAGAAAAATATTACATTTTTGTC
TTTGAAAAATTTGATCCAAATTTTGGTGCTTTCAAACATATTTGTGATATGAAGACTGTT
TATGCAATTGGCAGTAAACTCCTACTCAGTGGCCTCAATGAACCTCTTTTAATCCCTTCA
AGTTCTTTTCATGTATTCAGTCTTTTCATGAAAGAATTGCATATTTCACTAGCTTCTTAT
TCACGAGAACAAAAGCAGCATTACAAGACACTCATCACATATATGGGAGGAATTTGCCAT
ATTCCACTAAATAAACACATCACTCACTTAGTTACTGAAGATGTTTTCTCAAAAAAATAT
CGATATGCAGCTGACCAACAAATGGATATAAAAATTCTAAGAGCCACATGGATTGAAGAA
TCTTGGAAATATAGTGAAAAAAATCCTCTAAAAGTTGGAGCTGATAAAGAAAAATTTTAC
AAAAGTCATCAATTGAAAGTTTTCAATAACCTTGAAATTACAACAACTGGACTAACAAAT
GATGAAAAAGTAAAAGTACAAAAATTAGCAGAGAAAAATGGTGGAACTTTTAGCTCAGCA
TTTAAGACAATTTCAGCAAATGTTTTAATTTTGACCCCAAAAGACATCAATAGCGTAAAA
TACAAAGCAGCACAAAATCACAACATAAAATGCTTAGATTTTAAATGGATGACAGATTCA
GTGACAATTGGTTTCACTCAAGATCCTGAAAATTACAAAATTACCAAAAATAACCAAATC
AAATCATCAACACCAACAAAAACAACTGGTGATGTTTCTGCAATAAGAAATTTCAATTTT
GATAACACAATGTTGTCAGAAATTCATGAAAATACAGTAAAAAATTTCACAATTGATGAA
ACTAACAAACTTCAAAAAGGAATTTCAATTGCATCAACTACAATTTCATCTAGAGCTTCA
ACAGCTCATATGCAACCTCCAAAAGCATCAACAACTTTTAAAAAACCTGAAGCACCACCA
GCAAAAGTTGACGATGAAGTTGTAGTCATTCCACCATTTGAAAGTTCAGAAAATTCTGAA
GAAAGTTTCATACAAATTTTAGCTGATAAAATTGTTTGCATTTTTGGTTTTCAAAATGAT
ACTGATAGTATTTTATGCATAAAAGAATGTGAAAAACTTGGAGCATCACTTGTTGACATG
AATTATTCAAAAGTTGTCGATTTTGTCATTGCACCTTCAGATTTGATTTTAAATAAGGAA
CCAAATATGAAATATAAATATTTACTCAATGATGTTTGGTTAGAAGAATCAATTGATGAA
GGACGATGCATTTTACCACCAAAATTTTATCATTATGCTCTCTTTTATCTTCCTGAAAAA
GATAAAGTATTGAAATATGAAATTTTTGGTTGTTCAAATTATAAAGATCGTCAGCGACCT
TTTGTGAAATCTTTGATTGAAACTTTAGGTGGAACATTGAAAGATTCTTTTAGCAATTCT
GATCCAATTTTAATTTGTGAAGTTCCACAAGGTCAAAAATTCAAAGCAGCTTTAGCATGG
AAGAAAACTGTCCTAAAAGCTGATTGGCTCATTTCATGCTTTCAAAAAAGATCTCGAGTT
GATGAAAGAAATTTTTTAATTGGTGAAACAAAACCTTCGCTGAAAAATATTGAAAATGAT
GCAATTGATGACATTCCATATTCACAAGAAATTTCACAAGAAAATAAATCATCAGCGGTT
CAATCAGCACCAAGCACACCAATACGTAATGATGATGAGAAAGATGCTGAAACTTTGAGT
ATTTCTGTGTTATGTCAAGATTTACCAACTCCAGCTCGTGATATTACGAAAGCAATTTTA
AAAGAAAATCGAAGGCAAAGAAATGAAAACATGTCACCAAGGACAAAAAGATTAAAAGAT
TTATTAAAAACTCCAGGAATAAATGCTGATGTAAGTTCACCAGCACCAGCACTGCCGTCA
TGTATGAAAAAACCTGAAAGATGTTATGGATTTTTTAATGACGATTCTCCTTATACACAA
TATCAGTACAAATGCAAATTAGCAATTTTAGATGAAGATTATGTAGAAATTTCAAGCGAT
AAAAAGAAAAATTTAAAGAAAATTTGCTCAACGCCATCGGTTGACGATTGGAAAAAAGAT
TTCTTCAGACGAAGATTGCCAGAATTTGATTCACCAATGACAAAAGAAAATGAAATTGAA
TCACATGCAAATATGTCAAAAGAAGCTTCAAAATTTCTTAATTTTGGTGACACTGAAGTT
ATTAGTCCAAAAAGAAAATCAAATGAAATTGATGATTTTTCAAGTCTTGAAGAATTACTA
AAAGAAGCACAAGAAAATTCAGCTAAAAAAGCAAAAGCAAGTGAAAGACTTGAGTATGAA
AATCAACAAAAATCTGCAAAAAGTTTCCATGAAGAAATTGAAAATGAAAATAAAATTTTA
ATTGATCAACATCCAAGAAATGATCAAATAAATTGGACAAGCAGTCAAGTTGAAATTCCA
CGTGAAACTTCATCTTATCGGAATTCAAGTTTGGCATTTAGAAAATTAACTGAAATTGAC
TATGATGATGAAAATGCTGAAGAAATGGACAAACCTTGTACGAAATTTACTGAAAAAGTT
AATGAAGAAGAAGAAAGTGAAGAAATGAAGGAAAATGATGAAGAGAAAAATTCAATTATT
TTTGGAATAACATGTGGAAATGTCAGTGTTGAGACCAAAACAGAACTCTTTGAAAAAATC
CATCAACTTGGAGCTGAAGTTTCTGAAACAAATTTCAATCATTTAATCATCAGCAAACTT
GTGAGAAGTTCAAAATATTTTTCAGCATTAGCAGCTGGAATGAAAGTTCTTCATGCTGAT
TATTTAGATGCATGTTTAAAAGTACAAAAATTTGTCAATACTGATGAATTTGAAATTGGA
AATCCAAAATTTAAATGCAAATTTAGTGGAGTTAAAGATGAACTTTTACTTTCTGGACCT
TATAGATGTCGTTTATTAGTTGAAAGAAATTTTGATAAATTTAGTTCTGGATTATTTACA
GGAAAGAAATTTTTACTTTTTACAAGTGAAAATAGAAAGCAAGGAATAATTGACATTATT
GAATCTGGTGGTGGAAATGTTGTTGAAATTGGCTTAACTGTTTCATTATTAAAGAGGGAA
AATATTTTCATGTGCCTTGCTGATGATATGAAGAAATTAAGTGAAAAAGAAATTGTGGCT
CTTAAAGCATGCGATATCAAAATTCAAAGCACAAAATACATTTATGAACATTTACTGACT
GATAAAATTGTTTAA
>g15872.t1 Gene=g15872 Length=1164
MEQSIYNKQFDLTNQIFSEDNICYVYFVKHEKNSKDFMEDFQKFKDFHDQKNDSIIELID
EERCLKFTKEEIGEKYYIFVFEKFDPNFGAFKHICDMKTVYAIGSKLLLSGLNEPLLIPS
SSFHVFSLFMKELHISLASYSREQKQHYKTLITYMGGICHIPLNKHITHLVTEDVFSKKY
RYAADQQMDIKILRATWIEESWKYSEKNPLKVGADKEKFYKSHQLKVFNNLEITTTGLTN
DEKVKVQKLAEKNGGTFSSAFKTISANVLILTPKDINSVKYKAAQNHNIKCLDFKWMTDS
VTIGFTQDPENYKITKNNQIKSSTPTKTTGDVSAIRNFNFDNTMLSEIHENTVKNFTIDE
TNKLQKGISIASTTISSRASTAHMQPPKASTTFKKPEAPPAKVDDEVVVIPPFESSENSE
ESFIQILADKIVCIFGFQNDTDSILCIKECEKLGASLVDMNYSKVVDFVIAPSDLILNKE
PNMKYKYLLNDVWLEESIDEGRCILPPKFYHYALFYLPEKDKVLKYEIFGCSNYKDRQRP
FVKSLIETLGGTLKDSFSNSDPILICEVPQGQKFKAALAWKKTVLKADWLISCFQKRSRV
DERNFLIGETKPSLKNIENDAIDDIPYSQEISQENKSSAVQSAPSTPIRNDDEKDAETLS
ISVLCQDLPTPARDITKAILKENRRQRNENMSPRTKRLKDLLKTPGINADVSSPAPALPS
CMKKPERCYGFFNDDSPYTQYQYKCKLAILDEDYVEISSDKKKNLKKICSTPSVDDWKKD
FFRRRLPEFDSPMTKENEIESHANMSKEASKFLNFGDTEVISPKRKSNEIDDFSSLEELL
KEAQENSAKKAKASERLEYENQQKSAKSFHEEIENENKILIDQHPRNDQINWTSSQVEIP
RETSSYRNSSLAFRKLTEIDYDDENAEEMDKPCTKFTEKVNEEEESEEMKENDEEKNSII
FGITCGNVSVETKTELFEKIHQLGAEVSETNFNHLIISKLVRSSKYFSALAAGMKVLHAD
YLDACLKVQKFVNTDEFEIGNPKFKCKFSGVKDELLLSGPYRCRLLVERNFDKFSSGLFT
GKKFLLFTSENRKQGIIDIIESGGGNVVEIGLTVSLLKRENIFMCLADDMKKLSEKEIVA
LKACDIKIQSTKYIYEHLLTDKIV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g15872.t1 | Coils | Coil | Coil | 826 | 860 | - |
| 13 | g15872.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 17 | 125 | 6.0E-6 |
| 10 | g15872.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 127 | 225 | 2.2E-17 |
| 12 | g15872.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 228 | 324 | 1.4E-14 |
| 11 | g15872.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 421 | 513 | 1.3E-5 |
| 14 | g15872.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 519 | 612 | 1.1E-15 |
| 15 | g15872.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 953 | 1071 | 2.3E-18 |
| 22 | g15872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 631 | 647 | - |
| 23 | g15872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 631 | 653 | - |
| 5 | g15872.t1 | PANTHER | PTHR13561 | DNA REPLICATION REGULATOR DPB11-RELATED | 73 | 1043 | 4.5E-65 |
| 3 | g15872.t1 | Pfam | PF12738 | twin BRCT domain | 134 | 197 | 7.3E-9 |
| 2 | g15872.t1 | Pfam | PF12738 | twin BRCT domain | 232 | 296 | 4.0E-8 |
| 4 | g15872.t1 | Pfam | PF00533 | BRCA1 C Terminus (BRCT) domain | 531 | 594 | 1.8E-7 |
| 1 | g15872.t1 | Pfam | PF16770 | Regulator of Ty1 transposition protein 107 BRCT domain | 947 | 1038 | 2.5E-9 |
| 25 | g15872.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 118 | 201 | 11.309 |
| 27 | g15872.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 223 | 314 | 14.48 |
| 24 | g15872.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 538 | 607 | 14.397 |
| 26 | g15872.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 955 | 1039 | 10.252 |
| 19 | g15872.t1 | SMART | SM00292 | BRCT_7 | 127 | 205 | 8.4E-5 |
| 18 | g15872.t1 | SMART | SM00292 | BRCT_7 | 225 | 304 | 1.2E-6 |
| 20 | g15872.t1 | SMART | SM00292 | BRCT_7 | 521 | 597 | 1.1E-6 |
| 21 | g15872.t1 | SMART | SM00292 | BRCT_7 | 947 | 1029 | 0.51 |
| 17 | g15872.t1 | SMART | SM00292 | BRCT_7 | 1076 | 1161 | 34.0 |
| 8 | g15872.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 127 | 207 | 1.44E-16 |
| 7 | g15872.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 217 | 318 | 3.79E-13 |
| 9 | g15872.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 493 | 609 | 3.93E-16 |
| 6 | g15872.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 965 | 1045 | 5.38E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K10728 (topoisomerase (DNA) II binding protein 1)
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.
