RetrogeneDB ID: retro_pabe_1028

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:113661090..113663093(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PARP1
• Ensembl ID: ENSPPYG00000000164
• Aliases: None
• Description: poly (ADP-ribose) polymerase 1 [Source:HGNC Symbol;Acc:270]

Sequence

>retro_pabe_1028
ATGTTTGATGGAGAAGTCCCACACTGGTACCACTTCTCCTGCTTGCAGAAGGTGGGCCACTCCATGCGGCACCCTGACGT
TGAGGTGGATGGATTCTCTGAGCTTTGGTGGGATGACCAGCAGAAAGTCAAGAAGACAGCGGACCCTGGAGGAGTGACGG
GCAAAGGCCAGGATGGAATTGGTAGCAAGACAGAGAAGATGCTGGGTGACTGCAGCAGAGTAGGCCAAGTCCAACGGAAG
CAAGTGCAAGGGGTGTTATGGAGAAGATAGAAAAGGGCCACATGCGCCTATCCAAGAAGATGCTGGACCCTGAGAAGCCA
CAGCTAGGCATGATTGACCCCTAGTACCACCCAGGCTGCTTTGTCAAGAACAGGGAGGAGCTGGGTTTCCAGCCTGAGTA
CAGTGCGAGTCAGCTCAAGGGCTTCAGCCTCCTCGCTGCAGAGGATAAAGAAACCCTGAAGAAGCAGCTCCCAGGAGTCA
AGAGTGAAGGAAAGAGAGAAGGCGATGAGGTGGATGGAGTGGATGAAGTGGCCAAGAAGAAATCTAAAAAAGAAAAAGAC
GAGGATGGTAAGCTTGAAAAGGCCCTAAAGGCCCAGAACGACCTGATCTGGAACATCAAAGACGAGCTAAAGAAAGTGTG
TTCTACTAATGATCTGAAGGACATGCTCATCTTCAACAGGCAGCAGGTACCTTCCGGGGAGTCGGCAATCTTGGACCGAG
TAGCTGACAGCATGACGTTCGGTGCCCTCCTTCCCTGTGAGGAATGCTCAGGTCAGCTGGTCTTCAAGAGTGACACTTAT
TACTACACCGGGGATGTCACTGCCTGGACCAAGTGTATGGTCAAGACACGGACACCCAACCAGAAGGAACAGGTGATCCC
AAAGGAAGTCCAAGAAATCTCTTAACTCAAGAAATTTAAGGTTAAAAAGCAGGACTGTATATTCCCCTCAGAAACCAGTG
ACCCAGTGGCGGCCATGCCCCCACCCTCCACAGCCTCCGAGCCTGCTGCCATGAACGCCCCTGCTCCAGCAGATAAGCCA
TTATCCAACATGAAGATCCTTACTCTTGGGAAGCTCTCCTGGAACAAGGATGAAGTGAAGGCCATGATTGAGAAACTCAG
GGGAAAGTTGATGGGGACGGCCAACAAGGCTTCCCTGTGCATCAGCACTAAAGAGGAGGTGGAAAAGAAGAAGAAGAAGA
TGGAGGAAATGAAAGCCAACATCTGAGCTGTGTCTGAGGACTTCCTCCAGGACTTCTCTGCCTCCACCAAGGGGCTCCAG
GAGTTGTTCTCAGCGCACATCTTGTCCCCCTGGGGGGCAGAGGTGAAGGCAGAGCCTGTTGAAGTCGTAGCCCCAAGAGG
GAAGTCAGGAGCTGTGCTCTCCAAAAAAAGCAAGGGCCAGGTCGGGGAGGAAGGTATCAACAAATCTGAAAAGAGAATGA
AATTAACTCTTAAAGGAGGAGCAGCTGTGGATCCTGACTCTGGTCTGGAATACTCTGCGCATGTCCTGGAGAAAGGTGGG
AAGGTCTTCAGTGCCACCCTCAGCCTGGTGGACATCGTTAAAGGAACCAACTCCTATTACAAGCTGAAGTTGCTGAAGGA
TGACAGGGAAAGCAGGCATTGGATATTCAAGTCCTGAGACCGTGTGGGCACAGTGATTGGTAGCAACAGACTGGAACAGA
TGCTGCCCAAGGAGGACCCATTGAACACTTCATGAAATTATATGAAGAAACACTAGGAATGCTTGGCACTCCAAAAATTC
ACAAAGTATCCCAAAAAGTTCTACCCCCTGGAGATTGACTACGGCCAGGACAAAATGGTGGTGAAGAAGCTGACAGTAAA
TCCTGGCACCAAATCCATGCTCCTCAAGCCAGTTCAGGACCTCATCAAGATGATCTTTGATGTGGAAAGTATGAAGAAAG
CCATGGTGGGGTATGAGATCGACCTTCAGATGCCCTTGGGGAAGCTGAGCTAAAGGCAAATCCAGGCCGCATACTCCGTC
CTC

Alignment

ORF - retro_pabe_1028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.84 %
• Parental protein coverage: 69.03 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEAGGVTGKGQDGIGSKAEKTLGD
          MFDG.VPHWYHFSC..KVGHS.RHPDVEVDGFSEL.WDDQQKVKKTA..GGVTGKGQDGIGSK.EK.LGD
Retrocopy MFDGEVPHWYHFSCLQKVGHSMRHPDVEVDGFSELWWDDQQKVKKTADPGGVTGKGQDGIGSKTEKMLGD

Parental  FAAEYAKSNRSTCKG-CMEKIEKG-QVRLSKKMLDPEKPQLGMIDRWYHPGCFVKNREELGFRPEYSASQ
          .........R....G.C.....KG...RLSKKMLDPEKPQLGMID..YHPGCFVKNREELGF.PEYSASQ
Retrocopy -CSRVGQVQRKQVQG>CYGEDRKG>HMRLSKKMLDPEKPQLGMIDP*YHPGCFVKNREELGFQPEYSASQ

Parental  LKGFSLLATEDKEALKKQLPGVKSEGKRKGDEVDGVDEVAKKKSKKEKDKDSKLEKALKAQNDLIWNIKD
          LKGFSLLA.EDKE.LKKQLPGVKSEGKR.G..........KKKSKKEKD.D.KLEKALKAQNDLIWNIKD
Retrocopy LKGFSLLAAEDKETLKKQLPGVKSEGKREGXXXXXXXXXXKKKSKKEKDEDGKLEKALKAQNDLIWNIKD

Parental  ELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTK
          ELKKVCSTNDLK..LIFN.QQVPSGESAILDRVAD.M.FGALLPCEECSGQLVFKSD.YY.TGDVTAWTK
Retrocopy ELKKVCSTNDLKDMLIFNRQQVPSGESAILDRVADSMTFGALLPCEECSGQLVFKSDTYYYTGDVTAWTK

Parental  CMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPPETSAPVAATPPPSTASAPAAVNSSASADKPL
          CMVKT.TPN.KE.V.PKE..EIS.LKK.KVKKQD.IFP.ETS.PVAA.PPPSTAS.PAA.N..A.ADKPL
Retrocopy CMVKTRTPNQKEQVIPKEVQEIS*LKKFKVKKQDCIFPSETSDPVAAMPPPSTASEPAAMNAPAPADKPL

Parental  SNMKILTLGKLSRNKDEVKAMIEKLGGKLTGTANKASLCISTKKEVEKMNKKMEEVKEANIRVVSEDFLQ
          SNMKILTLGKLS.NKDEVKAMIEKL.GKL.GTANKASLCISTK.EVEK..KKMEE.K.ANI..VSEDFLQ
Retrocopy SNMKILTLGKLSWNKDEVKAMIEKLRGKLMGTANKASLCISTKEEVEKKKKKMEEMK-ANI*AVSEDFLQ

Parental  DVSASTKSLQELFLAHILSPWGAEVKAEPVEVVAPRGKSGAALSKKSKGQVKEEGINKSEKRMKLTLKGG
          D.SASTK.LQELF.AHILSPWGAEVKAEPVEVVAPRGKSGA.LSKKSKGQV.EEGINKSEKRMKLTLKGG
Retrocopy DFSASTKGLQELFSAHILSPWGAEVKAEPVEVVAPRGKSGAVLSKKSKGQVGEEGINKSEKRMKLTLKGG

Parental  AAVDPDSGLEHSAHVLEKGGKVFSATLGLVDIVKGTNSYYKLQLLEDDKENRYWIFRSWGRVGTVIGSNK
          AAVDPDSGLE.SAHVLEKGGKVFSATL.LVDIVKGTNSYYKL.LL.DD.E.R.WIF.S..RVGTVIGSN.
Retrocopy AAVDPDSGLEYSAHVLEKGGKVFSATLSLVDIVKGTNSYYKLKLLKDDRESRHWIFKS*DRVGTVIGSNR

Parental  LEQMPSKED-AIEHFMKLYEEKTG-NAWHSKN-FTKYPKKFYPLEIDYGQDEEAVKKLTVNPGTKSKLPK
          LEQM..KED..IEHFMKLYEE..G.NAWHSKN.FTKYPKKFYPLEIDYGQD...VKKLTVNPGTKS.L.K
Retrocopy LEQMLPKED<PIEHFMKLYEETLG<NAWHSKN<FTKYPKKFYPLEIDYGQDKMVVKKLTVNPGTKSMLLK

Parental  PVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSIL
          PVQDLIKMIFDVESMKKAMV.YEIDLQ.MPLGKLS.RQIQAAYS.L
Retrocopy PVQDLIKMIFDVESMKKAMVGYEIDLQ-MPLGKLS*RQIQAAYSVL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	123.24 RPM
SRP007412_cerebellum	0.12 RPM	118.07 RPM
SRP007412_heart	0.00 RPM	48.38 RPM
SRP007412_kidney	0.00 RPM	85.09 RPM
SRP007412_liver	0.03 RPM	72.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1028 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1028 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000016206	1 retrocopy	retro_ogar_2287,
Pongo abelii	ENSPPYG00000000164	1 retrocopy	retro_pabe_1028 ,