General information for g993.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein PAT1 homolog 1.
Parent gene
- The parent gene g993 is located on chr_3: 7306154..7306826 (+ 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_3 | g993 | g993.t1 | TSS | g993.t1 | 7303684 | 7303684 |
| chr_3 | g993 | g993.t1 | isoform | g993.t1 | 7303766 | 7306764 |
| chr_3 | g993 | g993.t1 | exon | g993.t1.exon1 | 7303766 | 7303804 |
| chr_3 | g993 | g993.t1 | cds | g993.t1.CDS1 | 7303766 | 7303804 |
| chr_3 | g993 | g993.t1 | exon | g993.t1.exon2 | 7303948 | 7304050 |
| chr_3 | g993 | g993.t1 | cds | g993.t1.CDS2 | 7303948 | 7304050 |
| chr_3 | g993 | g993.t1 | exon | g993.t1.exon3 | 7304155 | 7305815 |
| chr_3 | g993 | g993.t1 | cds | g993.t1.CDS3 | 7304155 | 7305815 |
| chr_3 | g993 | g993.t1 | exon | g993.t1.exon4 | 7305874 | 7306071 |
| chr_3 | g993 | g993.t1 | cds | g993.t1.CDS4 | 7305874 | 7306071 |
| chr_3 | g993 | g993.t1 | exon | g993.t1.exon5 | 7306150 | 7306395 |
| chr_3 | g993 | g993.t1 | cds | g993.t1.CDS5 | 7306150 | 7306395 |
| chr_3 | g993 | g993.t1 | exon | g993.t1.exon6 | 7306453 | 7306764 |
| chr_3 | g993 | g993.t1 | cds | g993.t1.CDS6 | 7306453 | 7306764 |
| chr_3 | g993 | g993.t1 | TTS | g993.t1 | 7307121 | 7307121 |
Sequences
>g993.t1 Gene=g993 Length=2559
ATGGCAGATTCTTTTTTCGGCTTTGACACAACATTACCGCGAGACGATGATTTGGGAAAT
TTGGGAAGAGAATTATCGGAAGATGAATATGATGCGCTTAACGATGAAACATTTAATCAT
GCTGTAAAGGATGATTGGGAAGATGGACATGAAACATTGGTGCGAATTAATCAATCAGCA
ACAATTGCTGGAAAATTGGAAGAATCGGATGATTATGACTCGGATTTGGATATCAATTTT
ATAACAAAATTGGATGATTTTGAAATCACTAATGATGATACTGACATAAGAAATCAATTT
CAACTAGATCCGAGTGTATGGACAACTCCAATTAAGCCAGTGACGCCAACTAAAGTTGCA
AACGTTTTTGGCAATAGTAAACTGCATGATGCTGAAGCTGCGAGGAAATTTCAAACAATT
CAACCACCGCCAGGTCTCGCATCACCATCATTAGCTCAGCAGACAAATGCATTGCAGCAA
CTTTTAGGCACAACAGCAGTTTCAAATACTGGTCCAAAGATTTTGTCAGTTGAGGAAATT
GAGAGGAATATCATCAATCAGCAACAGCAAAAAATGATTCAAGAAAAACTTGCTGCAATT
CAATCGAAAGTTCCTGCACAACAACAACAACAACAACAGTCAGTTCCTCCACCAGTTACG
ACAGCAAATCCTCAACAACCACAACAGCAACAACAGATGAGAAAAGTTCTGCCAAATCAA
CAACCTGCAGGTCTTATGTTTCAACCGCCTCCTCATCATCCAATCAATATGAATGGACCA
CCACCATTCAATATACCACCACATTTGCAAGGTCCAAATATGTCAAAATTCAATCCATTA
ATCAATCATCCGATGAATATGAATAATTTTCATCCAAATTTTGGCGGTCCAATGGGACCA
GGACCAATTAGACCACCACAGCAGTTGCCACCACAAATGAATCGAATGCCACCACATTTG
ATGCAAGGTGCACCATTAATGTATCCACAACAACAACAACAGCAAAATTCAGCGCAATTT
AATCAACGTTTATTGCAAGAAATTCAACAAAATCATCCAATGTTGAATCCAATGCAATTT
GCAATGAATCGTGGACAAATGCAGCAACAACTTCATCACCATCATCATCATAATAATAAC
AACAATAATAATATGAATAATGGTGCAAATAATCAACATCATCAACGTTTTAATAATGGT
AAAATGGAAGAATTTGATGAATATGCAAATCTCATGAGTAATCGAGATAAGCAATTTCTT
ATTACAATTCAATTGATGCAACTTAACACTGAAACGCCCTATTTTGATGATTATTATTAT
ACCATGTATAAAGAACGTCAACGTTTACGTGGCATTGAAAATGAAAGTCAAGCACATCGT
GATAATCAATTAAATCATCCTTTTACACAGCCCAAAGGTCACGCGCAAATGCTATTGCGA
CAATTTAATAATATTGGTAAGAATGGCATGCAAAATCAAAAGAATGGACTCGGACGTGAG
CGACATAATTCAGAATCATCGCAGAAAAATGAGAAGGAAAATCCCACGCCAAGAACCTAT
ACACCATTGCAATTTGAGAACTCACTTGGAAAATTACAATGTGGGAGTGTTACAGCACCA
AGAAAAATTATTGATATGGAAGTTGTTGGAAATGCTGAAAATGGACAAGGTGGTGTGTCC
GAATTGACAATTCAAAAAAGATCGAGACAAATTTTGATGCATATTGAGTTGCTTTATAAA
ATTGTGTTGAAACTTGAAGATTTACAACATCCTATGGCTATTGCTGCTTCTATTATTTTA
AAGGAAAAACGTGAAAAGCAACGTTTACAAATGGAGCAAGAAGCAAAAGAGAAACAAAAT
GAAGATGAGTCAAGCATTAGTTCAGCTAAATCATCAATTTCATTGAATGAACCAGAAACA
CAAAGTGAATTAATGACAAAATTGCTTGCATTGCTTTCGGTTGAAAAAGTGCCAGGAATT
ATGGCAGTACGCAAAGGAAGAGCACTTCTTAAGCGTCTTTTTCCTCACATTAAAGATCAA
CCAATACGCTGGGACATGTGGAATGCAATTTTCATCTCACTGACTGTGTTCAAGCGTGAT
AAATTGGAAGAGATTGAAGATTCTCTTATGGCCCTCTATTATGAGTTTGCAGTGCAATTG
CAGGATGCTGATTTCACTGACTTGCTTAAAATTACAAATAACATGATGACAAGTGAGAAA
TTAATGGGATATGTTAATGGCTGCAAGTTTGTTGTATCAAGCATAATCGCAATGATTATC
AAATGTGAGTTGCTTTACCAAAAATCAGGTGATTCAATAAACTTCAGTGAAGAAGAACAA
TGGATTCGTTTTCTCAATAAATTATTTGAGATTGTCAATAGTGATCGTACAGTTGATGCG
CAAATTTTAAGCTCAGCCAATAATGTTCATCGTGATAAAAATGATCATGATCGCATAATT
CGTACAGTTATTGCAAATTTTCAACGATTTAAGCCACGCTTCACTAGCGATGATGAGAAG
TTGGTGAAATTGTTGGGAATTCAGTATGATGTTAAATAA
>g993.t1 Gene=g993 Length=852
MADSFFGFDTTLPRDDDLGNLGRELSEDEYDALNDETFNHAVKDDWEDGHETLVRINQSA
TIAGKLEESDDYDSDLDINFITKLDDFEITNDDTDIRNQFQLDPSVWTTPIKPVTPTKVA
NVFGNSKLHDAEAARKFQTIQPPPGLASPSLAQQTNALQQLLGTTAVSNTGPKILSVEEI
ERNIINQQQQKMIQEKLAAIQSKVPAQQQQQQQSVPPPVTTANPQQPQQQQQMRKVLPNQ
QPAGLMFQPPPHHPINMNGPPPFNIPPHLQGPNMSKFNPLINHPMNMNNFHPNFGGPMGP
GPIRPPQQLPPQMNRMPPHLMQGAPLMYPQQQQQQNSAQFNQRLLQEIQQNHPMLNPMQF
AMNRGQMQQQLHHHHHHNNNNNNNMNNGANNQHHQRFNNGKMEEFDEYANLMSNRDKQFL
ITIQLMQLNTETPYFDDYYYTMYKERQRLRGIENESQAHRDNQLNHPFTQPKGHAQMLLR
QFNNIGKNGMQNQKNGLGRERHNSESSQKNEKENPTPRTYTPLQFENSLGKLQCGSVTAP
RKIIDMEVVGNAENGQGGVSELTIQKRSRQILMHIELLYKIVLKLEDLQHPMAIAASIIL
KEKREKQRLQMEQEAKEKQNEDESSISSAKSSISLNEPETQSELMTKLLALLSVEKVPGI
MAVRKGRALLKRLFPHIKDQPIRWDMWNAIFISLTVFKRDKLEEIEDSLMALYYEFAVQL
QDADFTDLLKITNNMMTSEKLMGYVNGCKFVVSSIIAMIIKCELLYQKSGDSINFSEEEQ
WIRFLNKLFEIVNSDRTVDAQILSSANNVHRDKNDHDRIIRTVIANFQRFKPRFTSDDEK
LVKLLGIQYDVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g993.t1 | Coils | Coil | Coil | 177 | 197 | - |
| 10 | g993.t1 | Coils | Coil | Coil | 599 | 622 | - |
| 6 | g993.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 208 | 236 | - |
| 7 | g993.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 496 | 519 | - |
| 8 | g993.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 498 | 512 | - |
| 4 | g993.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 609 | 638 | - |
| 5 | g993.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 609 | 624 | - |
| 2 | g993.t1 | PANTHER | PTHR21551 | TOPOISOMERASE II-ASSOCIATED PROTEIN PAT1 | 8 | 800 | 5.0E-88 |
| 3 | g993.t1 | PANTHER | PTHR21551:SF0 | PROTEIN ASSOCIATED WITH TOPO II RELATED-1, ISOFORM A | 8 | 800 | 5.0E-88 |
| 1 | g993.t1 | Pfam | PF09770 | Topoisomerase II-associated protein PAT1 | 15 | 758 | 2.4E-17 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0000290 | deadenylation-dependent decapping of nuclear-transcribed mRNA | BP |
KEGG
Orthology
- This transcript has been annotated with K12617 (DNA topoisomerase 2-associated protein PAT1)
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.
