RetrogeneDB ID: retro_pabe_2185

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b_random:757488..759399(-)
• 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_2185
ATGACAGTGCTGCAGGAACCTGTCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCAAGATGGGGTTTTCCT
CACAGAACGCCTTTATGCAGAAGTACACTCAGAAGAAGCCTTGTTTTTAATGGCGACCTGTTCTTACCTCCCAGGAAAGG
CCTATAAAGCATATAGACTCTTGAAAAGACACAGTAGTCCTACACCACAATGCAAATACCTGCTTGCAAAATGTTGTGTT
GATCTCAGTAAGCTTGCAGACTGGGAACAAATCTTATCTGGTAGAGTGTTTATTAAGCAGAAAAGCCATGATGATATTGT
TACTGAGTTTGGTGATTCAGTTTGCTTTCCCCTTCCATTGTTGGGACGTGTATATTGCAAGACAGATCGGCTTGCTAAAG
GATAAGAATATTACCAAAAGAGGCTTAGTTTAAATCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGGTGAA
AAGCCAGATCCTGACCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAGCACA
AGTACCTAATCACAGTTTATGTCACAGACAACCTGAGACCATTCTTATGGAAACACCCCAGGACACAACTGAGTTAAACA
GAGTCAATTTGGAATCTTCCAATTCAAAGTATCCTTGAATACAGATTCCCCAGTGTCTTTTATTGATTCAGCTGTAATTT
CACCTGAAACTGTCCCACTGGGAACAGGAACTTCCATATTATATAAACAGGTTCAAAATAAACCAAAAACTGGTCGAAGT
TTATTAACAGGACCAGCAGCTCTTAGTCCATTTACCCCACGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAGA
TGGATCTTATTTACAAAACTACACTAATACACCTTCTGTGATTGATGTGCCATCCACCAGAGCCCCTTCAAAAAAGTCTG
TTGCCAGAATTGGCCAAACTGGAGCAAAGTCTGTCTTCTCGCAGAGTGGAAATAGCCGAGAGGTAACTCCAATTCTTCCA
CTAACAGAAAGTTCTGGTCCATAAATAACTGCAACACCTCAGGTAATGAGCCCCACTATGACATCTCCCCCAAATGCACT
GCATCGAAGAAGTTCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGAGAATAGGAAGAAATTAAAAATGAAGTTTC
CACCTAAAATCCTAAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACTCAATCTAATATAAATGACAACCTG
AAAATTACAAAATTGGACTCTTCCATCAATTCAGAAGAGGAAATATCCACAATCACACCCAGATTCAGGCTTTTAATCTA
CAAAAAGCAGCAGCAGAAGGCTTGATGAGCCTTCTTCATGAAAGGGGGAAAGGTTATTTATCTTTATGTTCATACCACTG
CAAAGAAGCTATAAATATTTTGAGCCATCTACCTTCTCACCACTACAATACTGGTTGGGTACTATGCCAAATTGGAAGGT
CCTATTTTGAAATTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGTTAGAAGGATTGAGAATTATAGAGTCAAAG
GCATGGAAATCCACTCTACAACACTTTGGCATCTTCAAAAAGATGTCGCTCTTTCATTTCTGTCAAAAGACTTAACAGAC
ATGGATAAAAATTAGCCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACAGGAACACGATATTGCAATTAA
ATTCTTCCAGAGAGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTTTATTAGGGCGAGAGTTTGTCTTAACTG
AAGAAATGGACAAAGTGTTAGCTTGTTTTCGAAATGCTATTAGAGTCAATCCTAGACATTACAATGCATGG

Alignment

ORF - retro_pabe_2185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.18 %
• Parental protein coverage: 77.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEXHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          MTVLQEPVQAAIWQALNHYAY.D.VFL.ERLYAE.HSEEALFL.ATC.Y..GKAYKAYRLLK.HS..TPQ
Retrocopy MTVLQEPVQAAIWQALNHYAYQDGVFLTERLYAEVHSEEALFLMATCSYLPGKAYKAYRLLKRHSSPTPQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLLAKCCVDLSKLA..EQILSG.VF.KQKSHDDIVTEFGDS.CF.L.LLG.VYCKTDRLAKG.E.YQK
Retrocopy CKYLLAKCCVDLSKLADWEQILSGRVFIKQKSHDDIVTEFGDSVCFPLPLLGRVYCKTDRLAKG*EYYQK

Parental  SLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTI
          .LSLNPFLW.PFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCT.QVPNHSL.HRQPET.L.ETPQDT.
Retrocopy RLSLNPFLWYPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTAQVPNHSLCHRQPETILMETPQDTT

Parental  ELNRLNLESSNSKY-SLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLT
          ELNR.NLESSNSKY.SLNTDS.VS.IDSAVISP.TVPLGTGTSIL.KQVQNKPKTGRSLL.GPAALSP.T
Retrocopy ELNRVNLESSNSKY<SLNTDSPVSFIDSAVISPETVPLGTGTSILYKQVQNKPKTGRSLLTGPAALSPFT

Parental  PSFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQT
          P.FGILPLETPSPGDGSYLQNYTNTPSVIDVPST.APSKKSVARIGQ.G.KSVFSQSGNSREVTPIL..T
Retrocopy PRFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTRAPSKKSVARIGQTGAKSVFSQSGNSREVTPILPLT

Parental  QSSGPQTSTTPQVLSPTITSPTNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGIT
          .SSGP....TPQV.SPT.TSP.NAL.RRSS.LFTSDSSTTKEN.K....................KGGIT
Retrocopy ESSGP*ITATPQVMSPTMTSPPNALHRRSS*LFTSDSSTTKENRKXXXXXXXXXXXXXXXXXXXXKGGIT

Parental  QPNINDSLEITKLDSSIISEGKISTITP-QIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINIL
          Q.NIND.L.ITKLDSSI.SE..ISTITP.QIQAFNLQKAAAEGLMSLL.E.GKGYL.LCSY.CKEAINIL
Retrocopy QSNINDNLKITKLDSSINSEEEISTITP<QIQAFNLQKAAAEGLMSLLHERGKGYLSLCSYHCKEAINIL

Parental  SHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSE-VRRIENYRVEGMEIYSTTLWHLQKDVALSVLSK
          SHLPSHHYNTGWVLCQIGR.YFE.SEYMQAERIFSE.VRRIENYRV.GMEI.STTLWHLQKDVALS.LSK
Retrocopy SHLPSHHYNTGWVLCQIGRSYFEISEYMQAERIFSE<VRRIENYRVKGMEIHSTTLWHLQKDVALSFLSK

Parental  DLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNA
          DLTDMDKN.PEAWCAAGNCFSLQ.EHDIAIKFFQRAIQVDPNYAYAYTLLG.EFVLTEE.DK.LACFRNA
Retrocopy DLTDMDKN*PEAWCAAGNCFSLQQEHDIAIKFFQRAIQVDPNYAYAYTLLGREFVLTEEMDKVLACFRNA

Parental  IRVNPRHYNAW
          IRVNPRHYNAW
Retrocopy IRVNPRHYNAW

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_2185 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2185 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,