RetrogeneDB ID: retro_ptro_3295

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:16250239..16252149(+)
• Located in intron of: ENSPTRG00000040807

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC27
• Ensembl ID: ENSPTRG00000009326
• Aliases: None
• Description: None

Sequence

>retro_ptro_3295
ATGACGGTGCTGCAGGAACCCCTCCAGCCTGCTACATGGCAAGCACTAAACCACTATGCTTACCGAGATGGGGTTTTCCC
GGCAGAATGCCTTTATGCAGAAGTACACTCAGAAGAAGCCTTGTTTTTACTGGCTACCTGTTCTTACTACCCAGGAAAGG
CCTATAACACATATAGTCTCTTCAAAGTACACAGTTTTCCTACACTGCAATGCAAATACCTGCTTGCAAAATGTTGTGTT
GATCTCAGCAAGCTTGCAGAAGGGGAACAAATCTTATCTGGTGGAGTGTTCCATAAGCAGAAAAGCCATGATGATATTGT
TACCAAGTTTGGTGATTCAGCTTGCTTTCCCCTTCCATTGTTGGGACATGTATATTGCAAGACAGATCAGCTTGTCAAAG
GATCAGAATACTACCAAAAGTGCCTTAGTTTAAATCCTTTCCTCTGGTATCCCTTGAATCATTATGTGAAATAGATGAAA
AGCCAGATCCTGACCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAA
GTACCTAATCATAGTTTATGTCACAAACAGTCTGAGACCTTTCTTACGGAAACACCCCAGGACACAACTGAATTAAACAG
ATTGAATTTAGAATCTCCCAATTCAAAGTATTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTGTAATTT
CACGTGATACTGTCCAACTGGGAACAGGAACTTCCATATTATCAAACAGGTTCAAAATAAACCAAAAACTGGTCGAAGTT
TATTAAGAGGACCAGCAGCTCTTAGTCCATTAACCCCAAGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTTGAGAT
GGATCCTATTTCCAAAACTACACTGATACACCTTTTGTAATTGATGTGCCATCCACCGGAGCCCCTTCAAAAAAGTCTGT
TGCCAGAATTGGCCAAACTGGAGCAAAATCTGTCTTCTCACGGAGTGGAAATAGCCGAGAGGTAACTCCAATTCTTTCAC
AAACGGGAAGTCCTGGTCCATAAACAAGTACAACACCTCAGGTATTGAGCCCCACTATGACATCTCCCCCAAATGCACTG
CATCAAAAAAGTTCACAAGTCTTTACTAGTGACAGTTCCACAACCAAGAAGAATAGGAAGAAATTAAAAATGAAGTTTCC
ACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACAAATAAAGGAGGAATAACTCAGCCTCATATAAATGACAGCCTGG
AAATTACAAAATTGGACTCTTCCATCAATTCAGAAGGGAAAATATCCACAATCACACCTGAGATTCAGGTATTAATCTAC
AAAAAGCAGCAGCAGAAGGCTTGATGAGGCTTCTTCCTGAAAAGGGGAAAGGTTATTTAGCTTTGTGTTCATACCACTGC
AAAGAAGCTATAAATATTTTGAGCCATCTACCTTCTCACCACTACAATTCTGGTTGGGTACTGTGCCAAATTGGAAGGGT
CTATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGGATTATAGAGTCAAAG
CCATGGAAATCTACTCTACAACACTTTGGCATCTTCAAAAACATGTTGCTCTTTCAGTTCTGTCAAAAGACTTAACAGAC
ATGGATAAAAATTCACCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTTAGTCTGCAACAGGAACACGATATTGCAATTAA
ATTCCTCCAGAGAGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTCTATTAGGGCATGAGTTTGTCTTAACTG
AAGAATGGACAAAGCATTAGCTTGTTTTTGAAATACTATCAGAGTCAATCCTAGACATTATAATGTATGG

Alignment

ORF - retro_ptro_3295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 77.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEVHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          MTVLQEP.Q.A.WQALNHYAYRD.VF.AE.LYAEVHSEEALFLLATC.Y..GKAY..Y.L.K.HS..T.Q
Retrocopy MTVLQEPLQPATWQALNHYAYRDGVFPAECLYAEVHSEEALFLLATCSYYPGKAYNTYSLFKVHSFPTLQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLLAKCCVDLSKLAEGEQILSGGVF.KQKSHDDIVT.FGDSACF.L.LLGHVYCKTD.L.KGSE.YQK
Retrocopy CKYLLAKCCVDLSKLAEGEQILSGGVFHKQKSHDDIVTKFGDSACFPLPLLGHVYCKTDQLVKGSEYYQK

Parental  SLSLNPFLWSPF-ESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDT
          .LSLNPFLW.P..ESLCEI.EKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSL.H.Q.ET.LTETPQDT
Retrocopy CLSLNPFLWYPL<ESLCEIDEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLCHKQSETFLTETPQDT

Parental  IELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILS-KQVQNKPKTGRSLLGGPAALSPL
          .ELNRLNLES.NSKYSLNTDS.VS.IDSAVIS.DTV.LGTGTSILS.KQVQNKPKTGRSLL.GPAALSPL
Retrocopy TELNRLNLESPNSKYSLNTDSPVSSIDSAVISRDTVQLGTGTSILS<KQVQNKPKTGRSLLRGPAALSPL

Parental  TPSFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQ
          TPSFGILPLETPSP.DGSY.QNYT.TP.VIDVPSTGAPSKKSVARIGQTG.KSVFS.SGNSREVTPIL.Q
Retrocopy TPSFGILPLETPSP*DGSYFQNYTDTPFVIDVPSTGAPSKKSVARIGQTGAKSVFSRSGNSREVTPILSQ

Parental  TQSSGPQTSTTPQVLSPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGI
          T.S.GP.TSTTPQVLSPT.TSPPNAL...SS..FTSDSSTTK.N.KKLKMKFP..............GGI
Retrocopy TGSPGP*TSTTPQVLSPTMTSPPNALHQKSSQVFTSDSSTTKKNRKKLKMKFPXXXXXXXXXXXXXXGGI

Parental  TQPNINDSLEITKLDSSIISEGKISTITPQIQAF-NLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINI
          TQP.INDSLEITKLDSSI.SEGKISTITP.IQ...NLQKAAAEGLM.LL.E.GKGYLALCSY.CKEAINI
Retrocopy TQPHINDSLEITKLDSSINSEGKISTITPEIQVL<NLQKAAAEGLMRLLPEKGKGYLALCSYHCKEAINI

Parental  LSHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSK
          LSHLPSHHYN.GWVLCQIGR.YFELSEYMQAERIFSEVRRIE.YRV..MEIYSTTLWHLQK.VALSVLSK
Retrocopy LSHLPSHHYNSGWVLCQIGRVYFELSEYMQAERIFSEVRRIEDYRVKAMEIYSTTLWHLQKHVALSVLSK

Parental  DLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEE-LDKALACFRN
          DLTDMDKNSPEAWCAAGNCFSLQ.EHDIAIKF.QRAIQVDPNYAYAYTLLGHEFVLTEE..DKALACF.N
Retrocopy DLTDMDKNSPEAWCAAGNCFSLQQEHDIAIKFLQRAIQVDPNYAYAYTLLGHEFVLTEE<MDKALACF*N

Parental  AIRVNPRHYNAW
          .IRVNPRHYN.W
Retrocopy TIRVNPRHYNVW

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	31.05 RPM
SRP007412_cerebellum	0.00 RPM	34.49 RPM
SRP007412_heart	0.00 RPM	34.54 RPM
SRP007412_kidney	0.00 RPM	25.21 RPM
SRP007412_liver	0.00 RPM	17.94 RPM
SRP007412_testis	0.00 RPM	79.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3295 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3295 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,