RetrogeneDB ID: retro_pabe_3592

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:39009541..39011434(-)
• 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_3592
CCTGTCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGGGGTTTTCCTCACAGAACGCCTTTATGC
AGAAGTACACTCAGAAGAAGCCTTGTTTTTAATGGCGACCTGTTCTTACCTCCCAGGAAAGGCCTATAAAGCATATAGAC
TCTTGAAAAGACACAGTAGTCCTACACTGCAATGCAAATACCTGCTTGCAAAATGTGTTGATCTCAGTAAGCTTGCAGAC
TGGGAACAAATCTTATCTGGTGGAGCGTTTAATAAGCAGAAAAGCCATGATAATATTGTTACTGAGTTTGGTGATTCAGT
TTGCTTTCCCCTTCCATTGTTGGGACGTGCATATTGCAAGACAGATCGGCTTGCTAAAGGATAAGAATGTTACCAAAAGA
GGCTTAGTTTAAATCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACA
TTTAAATACATATCTTTGCAGAACTTTAGCAACTGTCTGCCCAACTCTTGAACAACACAAGTACCTAATCACAGTTTATG
TCACAGACAACCTGAGACCATTCTTATGGAAACACCCCAGGACACAACTGAATTAAACAGAGTCAATTTAGAATCTTCCA
ATTCAAAGTACTCCTTGAATACAGATTCCCCAGTGTCTTTTATTGATTCAGCTGTAATTTCACCTGAAACTGTCCCACTG
GGAACAGGAAATTCCATATTATCTAAACAGGTTCAAAATAAACCAAAAACTGGTCGAAGTTTATTAACAGGACCAGCAGC
TCTTAGTCCATTTACCCCACGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAGACGGATCTTATTTACAAAACT
ACACTAATACACCTTCTGTAATTGATGTGCCATCCACCAGAGCCCCTTCAAAAAAGTCTGTTGCCAGAATTGGCCAAACT
GGAGCAAAGTCTGTCTTCTCACAGAGTGGAAATAGTCGAGAGGTAACTCCAATTCTTCCACTAACAGAAAGTTCTGGTCC
ATAAATAACTACAACACCTCAGGTAATGAGCCCCACTATGACATCTCCCCCAAATGCACTGCATCGAAGAAGTTCATGAG
TCTTTACTAGTGACAGTTCCAAAACCAAGGAGAATAGGAAGAAATTAAAAATGAAGGTTCCACCTAAAATCCTAAACAGA
AAAACAAAAAGTAAAACTAATGAAGGAGGAATAACTCAATCTAATATAAATGACAACCTGGAAATTACAAAATTGGACTC
TTCCATCAATTCAGAAGAGGAAATATCCACAATCACACCTCAGATTCAGGTTTTTAATCTACAAAAAGCAGCAGCAGAAG
GCTTGATGAGCCTTCTTCATGAAAGGGGGAAAGGTTATTTAGCTTTATGTTCATACCACTGCAAAGAAGCTATAAATATT
TTGAGCCATCTACCTTCTCACCACTACAATACTGGTTGGGTACTGTGCCAAATTGGAAGGTCCTATTTTGAACTTTCAGA
GTACATGCAAGCTGAAAGAATATTCTCAGAGATTAGAAGGATTGAGAATTATAGAGTCAAAGGCAAGGAAATCTACTCTA
CAACACTTTGGCATCTTCAAAAAGATGTCGCTCTTTCATTTCTGTCAAAAGACTTAACAGACATGGATAAAAATTCGCCA
GAGGCCTGGTGTTCTGCAGGGAACTGTTTCAGTCTGCAACGGGAACACGATATTGCAATTAAATTCTTCCAGAGAGCTAT
CCAAGTGGATCCAAATTATGCTTATGCCTATACTTTATTAGGGCGAGAGTTTGTCTTAACTGAAGAATTGGACAAAGTGT
TAGCTTGTTTTCAAAATGCTATCAGAGTCAATCCTAGACATTACAATGCATGG

Alignment

ORF - retro_pabe_3592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.97 %
• Parental protein coverage: 76.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVQAAIWQALNHYAYRDAVFLAERLYAEXHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQCKYLLA
          PVQAAIWQALNHYAYRD.VFL.ERLYAE.HSEEALFL.ATC.Y..GKAYKAYRLLK.HS..T.QCKYLLA
Retrocopy PVQAAIWQALNHYAYRDGVFLTERLYAEVHSEEALFLMATCSYLPGKAYKAYRLLKRHSSPTLQCKYLLA

Parental  KCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQKSLSLNP
          KC.VDLSKLA..EQILSGG.FNKQKSHD.IVTEFGDS.CF.L.LLG..YCKTDRLAKG.ECYQK.LSLNP
Retrocopy KC-VDLSKLADWEQILSGGAFNKQKSHDNIVTEFGDSVCFPLPLLGRAYCKTDRLAKG*ECYQKRLSLNP

Parental  FLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTIELNRLN
          FLW.PFESLCEIGEKPDPDQTFK..SLQNFSNCLPNS.TTQVPNHSL.HRQPET.L.ETPQDT.ELNR.N
Retrocopy FLWYPFESLCEIGEKPDPDQTFKYISLQNFSNCLPNS*TTQVPNHSLCHRQPETILMETPQDTTELNRVN

Parental  LESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTPSFGILP
          LESSNSKYSLNTDS.VS.IDSAVISP.TVPLGTG.SILSKQVQNKPKTGRSLL.GPAALSP.TP.FGILP
Retrocopy LESSNSKYSLNTDSPVSFIDSAVISPETVPLGTGNSILSKQVQNKPKTGRSLLTGPAALSPFTPRFGILP

Parental  LETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQTQSSGPQT
          LETPSPGDGSYLQNYTNTPSVIDVPST.APSKKSVARIGQ.G.KSVFSQSGNSREVTPIL..T.SSGP..
Retrocopy LETPSPGDGSYLQNYTNTPSVIDVPSTRAPSKKSVARIGQTGAKSVFSQSGNSREVTPILPLTESSGP*I

Parental  STTPQVLSPTITSPTNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQPNINDS
          .TTPQV.SPT.TSP.NAL.RRSS..FTSDSS.TKEN.K.....................GGITQ.NIND.
Retrocopy TTTPQVMSPTMTSPPNALHRRSS*VFTSDSSKTKENRKXXXXXXXXXXXXXXXXXXXXEGGITQSNINDN

Parental  LEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSHLPSHHY
          LEITKLDSSI.SE..ISTITPQIQ.FNLQKAAAEGLMSLL.E.GKGYLALCSY.CKEAINILSHLPSHHY
Retrocopy LEITKLDSSINSEEEISTITPQIQVFNLQKAAAEGLMSLLHERGKGYLALCSYHCKEAINILSHLPSHHY

Parental  NTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTDMDKNS
          NTGWVLCQIGR.YFELSEYMQAERIFSE.RRIENYRV.G.EIYSTTLWHLQKDVALS.LSKDLTDMDKNS
Retrocopy NTGWVLCQIGRSYFELSEYMQAERIFSEIRRIENYRVKGKEIYSTTLWHLQKDVALSFLSKDLTDMDKNS

Parental  PEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRVNPRHYN
          PEAWC.AGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLG.EFVLTEELDK.LACF.NAIRVNPRHYN
Retrocopy PEAWCSAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGREFVLTEELDKVLACFQNAIRVNPRHYN

Parental  AW
          AW
Retrocopy AW

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	0.00 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_3592 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3592 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3592 has 0 orthologous retrocopies within eutheria group .

---

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,