RetrogeneDB ID: retro_pabe_3607

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:64739902..64741816(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC27
• Ensembl ID: ENSPPYG00000008945
• Aliases: None
• Description: cell division cycle 27 [Source:HGNC Symbol;Acc:1728]

Sequence

>retro_pabe_3607
ATGACAGTGCTGCAGGAACCCGTTCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGGGGTTTTCCT
CACAGAACGCCTTTATGCAGAAGTACACTCAGAAGAAGCTTTGTTTTTAATGGCGACCTGTTCTTACCTCCCAGGAAAGG
CCTATAAAGCATATAGACTCTTGAATAGACATAGTTGTCCTACACCACAATGCAAATACCTGCTTGCAAAATGTTGTGTT
GATCTCAGTAAGCTTGCAGACTGGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGT
TACTGAGTTTGGTGATTCAGTTTGCTTTCCCCTTCCATTGTCAGGACGTGTATATTGCAAGACAGATCGGCTTGCTAAAG
GATAAGAATGTTACCAAAAGAGACTTAGTTTAAATCCTTTCCTCTGGTATCCCTTTGAATCGTTAGGTGAAATAGGTGAA
AAGCCAGATCCTGGCCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACA
AGTACCTAATCACAGTTTATGTCACAGACAGCCTGAGACCATTCTTATGGAAACACCCCAGGACACAACTGAATTAAACA
GAGTCAGTTTAGAATCTTCCAATTCAAAGTACTCCTTGAATACAGATTCCCCAGTGTCTTTTATTGATTCAGCTGTAATT
TCACCTGAAACTATCCCACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAATAAACCAAAAACTGGTCAAAG
TTTATTAACAGGACCAGCAGCTCTTAGTCCATTTACCCCAAGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAG
ATGGATCTTATTTACAAAACTACACTAATACACCTTCTGTAATTGATGTGCCATCCACTGGAGCCCCTTCAAAAAAGTCT
GTTGCCAGAATTGGCCAAACTGGAGCAAAGTCTGTCTTCTCACAGAGTGGAAATAGCCGAGAGGTAACTCCAATTCTTTC
ACTAACAGAAAGTTCTGGTCCATAAATAACTACAACACCTCAGGTAATGAGCCCCACTATCACATCTCCCCCAAATGCAC
GGCATCGAAGAAGTTCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGAGAATAGGAAGAAATTAAAAATGAAGTTT
CCACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACTCAATCTAATATAAATGACAACCT
GGAAATTACAAAATTGGACCCTTCCATCAATTCAGAAGAGGAAATATCCACAATCACACCTCAGATTCAGGCTTTTCATC
TACAAAAAGCAGCAGCAGAAGGCTTGATGAGCCTTCTTCATGAAAGGGGGAAAGGTTATTTAGCTTTATGTTCATGCCAC
TGCAAAGAAGCTATAAATATTTTGAGCCATCTACCTTCTCACCACTTCAATACTGGTTGGGTACTTTGCCAAATTGGAAG
GTCCTATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGAGTCG
AAGGCATGGAAATCTACTCTACAACACTTTGGCATCTTCAAAAAGATGTCGCTCTTTCATTTCTGTCAAAAGACTTAACA
GACACGGATAAAAATTCGCCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACAGGAACACGATATTGCAAT
TAAATTCTTCCAGAGAGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTTTATTAGGGCGAGAGTTTGTCTTAA
CTGAAGAATTGGACAAAGCATTAGCTTGTATTCGAAATGCTATCAGAGTCAGTCCTAGACATTACAATGCATGG

Alignment

ORF - retro_pabe_3607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.34 %
• Parental protein coverage: 77.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEXHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          MTVLQEPVQAAIWQALNHYAYRD.VFL.ERLYAE.HSEEALFL.ATC.Y..GKAYKAYRLL..HSC.TPQ
Retrocopy MTVLQEPVQAAIWQALNHYAYRDGVFLTERLYAEVHSEEALFLMATCSYLPGKAYKAYRLLNRHSCPTPQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLLAKCCVDLSKLA..EQILSGGVFNKQKSHDDIVTEFGDS.CF.L.L.G.VYCKTDRLAKG.ECYQK
Retrocopy CKYLLAKCCVDLSKLADWEQILSGGVFNKQKSHDDIVTEFGDSVCFPLPLSGRVYCKTDRLAKG*ECYQK

Parental  SLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTI
          .LSLNPFLW.PFESL.EIGEKPDP.QTFKFTSLQNFSNCLPNSCTTQVPNHSL.HRQPET.L.ETPQDT.
Retrocopy RLSLNPFLWYPFESLGEIGEKPDPGQTFKFTSLQNFSNCLPNSCTTQVPNHSLCHRQPETILMETPQDTT

Parental  ELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTP
          ELNR..LESSNSKYSLNTDS.VS.IDSAVISP.T.PLGTGTSILSKQVQNKPKTG.SLL.GPAALSP.TP
Retrocopy ELNRVSLESSNSKYSLNTDSPVSFIDSAVISPETIPLGTGTSILSKQVQNKPKTGQSLLTGPAALSPFTP

Parental  SFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQTQ
          SFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQ.G.KSVFSQSGNSREVTPIL..T.
Retrocopy SFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQTGAKSVFSQSGNSREVTPILSLTE

Parental  SSGPQTSTTPQVLSPTITSPTNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQ
          SSGP...TTPQV.SPTITSP.NA..RRSS.LFTSDSSTTKEN.KKLKMKFPPKIPNRKTKSKTNKGGITQ
Retrocopy SSGP*ITTTPQVMSPTITSPPNARHRRSS*LFTSDSSTTKENRKKLKMKFPPKIPNRKTKSKTNKGGITQ

Parental  PNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSH
          .NIND.LEITKLD.SI.SE..ISTITPQIQAF.LQKAAAEGLMSLL.E.GKGYLALCS..CKEAINILSH
Retrocopy SNINDNLEITKLDPSINSEEEISTITPQIQAFHLQKAAAEGLMSLLHERGKGYLALCSCHCKEAINILSH

Parental  LPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLT
          LPSHH.NTGWVLCQIGR.YFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALS.LSKDLT
Retrocopy LPSHHFNTGWVLCQIGRSYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSFLSKDLT

Parental  DMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRV
          D.DKNSPEAWCAAGNCFSLQ.EHDIAIKFFQRAIQVDPNYAYAYTLLG.EFVLTEELDKALAC.RNAIRV
Retrocopy DTDKNSPEAWCAAGNCFSLQQEHDIAIKFFQRAIQVDPNYAYAYTLLGREFVLTEELDKALACIRNAIRV

Parental  NPRHYNAW
          .PRHYNAW
Retrocopy SPRHYNAW

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	43.24 RPM
SRP007412_cerebellum	0.00 RPM	52.05 RPM
SRP007412_heart	0.00 RPM	16.95 RPM
SRP007412_kidney	0.03 RPM	14.25 RPM
SRP007412_liver	0.00 RPM	15.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3607 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3607 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3607 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000004897	3 retrocopies	retro_hsap_2159, retro_hsap_4333, retro_hsap_4933,
Pongo abelii	ENSPPYG00000008945	35 retrocopies	retro_pabe_2094, retro_pabe_2169, retro_pabe_2170, retro_pabe_2172, retro_pabe_2178, retro_pabe_2182, retro_pabe_2183, retro_pabe_2184, retro_pabe_2185, retro_pabe_2186, retro_pabe_2190, retro_pabe_2192, retro_pabe_3526, retro_pabe_3545, retro_pabe_3547, retro_pabe_3550, retro_pabe_3551, retro_pabe_3553, retro_pabe_3556, retro_pabe_3582, retro_pabe_3583, retro_pabe_3589, retro_pabe_3592, retro_pabe_3598, retro_pabe_3599, retro_pabe_3603, retro_pabe_3605, retro_pabe_3606, retro_pabe_3607 , retro_pabe_3609, retro_pabe_3610, retro_pabe_3827, retro_pabe_3828, retro_pabe_3833, retro_pabe_3834,
Pan troglodytes	ENSPTRG00000009326	9 retrocopies	retro_ptro_1644, retro_ptro_2972, retro_ptro_3053, retro_ptro_3071, retro_ptro_3072, retro_ptro_3288, retro_ptro_3294, retro_ptro_3295, retro_ptro_3304,