General information for g9941.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA topoisomerase 2-binding protein 1.
Parent gene
- The parent gene g9941 is located on chr_1: 6122938..6124740 (+ 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_1 | g9941 | g9941.t1 | TSS | g9941.t1 | 6120988 | 6120988 |
| chr_1 | g9941 | g9941.t1 | isoform | g9941.t1 | 6121056 | 6122938 |
| chr_1 | g9941 | g9941.t1 | exon | g9941.t1.exon1 | 6121056 | 6121169 |
| chr_1 | g9941 | g9941.t1 | cds | g9941.t1.CDS1 | 6121056 | 6121169 |
| chr_1 | g9941 | g9941.t1 | exon | g9941.t1.exon2 | 6121226 | 6121356 |
| chr_1 | g9941 | g9941.t1 | cds | g9941.t1.CDS2 | 6121226 | 6121356 |
| chr_1 | g9941 | g9941.t1 | exon | g9941.t1.exon3 | 6121420 | 6122938 |
| chr_1 | g9941 | g9941.t1 | cds | g9941.t1.CDS3 | 6121420 | 6122938 |
| chr_1 | g9941 | g9941.t1 | TTS | g9941.t1 | NA | NA |
Sequences
>g9941.t1 Gene=g9941 Length=1764
ATGGAAACTACTGAAACCGTATACAAGTTTATTCAGAATTTGGAAAAAACTACTATTATA
GTCTTTGTAAAGGAGCGTGATGGAATGACAGAAAGAATGAAAAAAATATACGAGCAAACT
AAAGAAATATGCAATGCTGATATAAGAAGAATGTCAATTGATGAAGTGTTGATGCTTAGA
AATGCAATTTTATCGCTCAATCCTCATATATTTATACTTAGTGAATTCAATGGCGAAGTT
TATAGTTACTTGGATAATATTGAAAATAATCATATGATTCTGGGAGTATCATTTATGGAA
AGCATACTTGAGTTAAAAGAAAAAGAGTATATCACTATTCCTACAAATCATCGCCAAATA
TTCAATGCAGCCTTTAATGATGTTAACTTGTGCGTTTCAAATATTCGTACTGCAGAAAAG
AAAGAAATTGCAAAAATGTTAAAGCTTATGAATGGAAAAATATCAGATAAAATAGATTCG
AATGTTACTCATCTCATTACGAACACTACAAAATCTGTCAAATATCTTGAGGCTGCAGCA
AATAAAATTCCAATTTATCATTATCAATGGGTGCAAAATGTATGGAAAAAATGTTTAAAA
GAGAAAGATCATAGCATTCGAGCTGTTTCTTCAATATTTGACATTTATAAATTGCCACCT
TTCTTTGATTTGAAAATCGCATGTACTGGTGTTGGAAAAGAAGAAAAAAAGTGTTTGGAA
ACGTTGATTGAAGAAAATGGAGGAGAATTCGCTGAAACATACAATTCTGCAAGTACTGAT
ATTTTACTTATTAAGCGAAAAGATCCAACCAATCCGAAATATCAAAATGCTGTTAAACGT
AAAATTCCAATTTTAAAATGTGAATGGGTAGAAGAAAGTGTCAAAGCTGGCTACTCATTG
GCATATGAAGATTTTTGTTTCAAAAGCAGTTCACCAAGAGACAGTAAACATAAAAAGAAA
GAAAATGAGGCTAATTCATCAGCATCAGATCAATCATTTGATACGCAATCTGATGTCAGT
TTTAACACAACTGCAAATAGCATTAGTACAACCGCAACTAGCGTGAGCACTATGCAGCGA
GTGCCTTCTGTTGCATCAATTCGATCTAACGTGCTTAAAGAAAGAAAGACATCTATAGAA
TTTATCAAAAATTTTGCTGTTCAGCAACTTAAGAAATTGGATAACTTTCTTGATGGCTAT
ACATTTTATTTAAAAGATTATCCGGAAGAAATTTTTGCAAAAATGCGACGAATAATAACT
AGATGTGGTGGATCAAGCGTGGATAATTTAAATCAGAGATTTACTCATGTCTTGTGCTAT
GGTGATGTGAATTTGAAGAACCTTTCTAAGATGCTGTATGAGAAAGATAATTGTGCTGTC
CCTGTTCGTGCTGAGTGGTTAGTTGATTGTTTAACAAAAATGGAACCATTACAAGAAACA
GATTATATTATTGATTTAAGCGCTTATGAAGTCAAACGAGTGCCATCATCACCTTTCACA
AAGAAAACATTAAGTATGCTTAGAATAATTGCACAACAAAAGAAAGATGAAGAAAATACT
ATGATGATGCCACCGCCATCAAAAATAGAAACTTCAAGCACCACAGATGAACGTGTTGTA
GAATTTAAGCAAACTTTAATTGAAACTAATCATAAAAAAGTTAAACAACCACTGACAAAC
ACTGTAAAGGGAAAACGATCAAGTGAAGAAGATATTAGTGTCTTGTATAATAACAAAAGA
CGAAAACTTTTTGAGTCAAGTTAA
>g9941.t1 Gene=g9941 Length=587
METTETVYKFIQNLEKTTIIVFVKERDGMTERMKKIYEQTKEICNADIRRMSIDEVLMLR
NAILSLNPHIFILSEFNGEVYSYLDNIENNHMILGVSFMESILELKEKEYITIPTNHRQI
FNAAFNDVNLCVSNIRTAEKKEIAKMLKLMNGKISDKIDSNVTHLITNTTKSVKYLEAAA
NKIPIYHYQWVQNVWKKCLKEKDHSIRAVSSIFDIYKLPPFFDLKIACTGVGKEEKKCLE
TLIEENGGEFAETYNSASTDILLIKRKDPTNPKYQNAVKRKIPILKCEWVEESVKAGYSL
AYEDFCFKSSSPRDSKHKKKENEANSSASDQSFDTQSDVSFNTTANSISTTATSVSTMQR
VPSVASIRSNVLKERKTSIEFIKNFAVQQLKKLDNFLDGYTFYLKDYPEEIFAKMRRIIT
RCGGSSVDNLNQRFTHVLCYGDVNLKNLSKMLYEKDNCAVPVRAEWLVDCLTKMEPLQET
DYIIDLSAYEVKRVPSSPFTKKTLSMLRIIAQQKKDEENTMMMPPPSKIETSSTTDERVV
EFKQTLIETNHKKVKQPLTNTVKGKRSSEEDISVLYNNKRRKLFESS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g9941.t1 | CDD | cd00027 | BRCT | 128 | 193 | 1.9972E-14 |
| 10 | g9941.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 121 | 219 | 7.2E-20 |
| 9 | g9941.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 221 | 320 | 1.1E-16 |
| 8 | g9941.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 373 | 486 | 1.8E-15 |
| 15 | g9941.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 316 | 337 | - |
| 4 | g9941.t1 | PANTHER | PTHR13561 | DNA REPLICATION REGULATOR DPB11-RELATED | 57 | 549 | 4.0E-50 |
| 2 | g9941.t1 | Pfam | PF00533 | BRCA1 C Terminus (BRCT) domain | 125 | 192 | 3.3E-11 |
| 3 | g9941.t1 | Pfam | PF00533 | BRCA1 C Terminus (BRCT) domain | 219 | 293 | 4.6E-8 |
| 1 | g9941.t1 | Pfam | PF16589 | BRCT domain, a BRCA1 C-terminus domain | 396 | 482 | 4.0E-7 |
| 16 | g9941.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 120 | 191 | 13.145 |
| 17 | g9941.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 216 | 307 | 14.258 |
| 18 | g9941.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 392 | 484 | 14.619 |
| 13 | g9941.t1 | SMART | SM00292 | BRCT_7 | 122 | 198 | 1.5E-9 |
| 14 | g9941.t1 | SMART | SM00292 | BRCT_7 | 218 | 297 | 7.1E-9 |
| 12 | g9941.t1 | SMART | SM00292 | BRCT_7 | 394 | 474 | 0.024 |
| 7 | g9941.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 125 | 206 | 1.74E-16 |
| 6 | g9941.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 218 | 308 | 6.94E-16 |
| 5 | g9941.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 387 | 485 | 2.36E-15 |
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.
