RetrogeneDB ID: retro_ptro_3288

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:7251192..7253097(+)
• Located in intron of: None

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_3288
ATGATGGTGCTGCAGGAACCCGTCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGTTGGTGCTTTCCT
CGCAAAACCCCTTATGCAGAAGTACACACAGAAGAAGCTTTGTTTTTACTGGCAACCTGTTCTTACCGCCCAGGAAAGGA
CTATAAAGCATATAGACTCTTGAAAGGACTCAGTTGTGCTGCACTGCAATGCAAATACCTGCTTGAAAAATGTTATGTTG
ATCTCAGCAAGCTTGCAGAAGGAGAACAAATCTTATCTGGTGGAGTGTTTAATAAGTAGAAAAGCCATGATGATATTGTT
ACTGAGTTTGGTGATTCAGCTTGCTTTCCCCTTCCATTGCTGGGACATGTATACTGCAAGACAGATTGGCTTGCCAAAGG
ATTAGAATGTTACCAAAAGAGCCTTAGTTTAAATCCTTTCTTCTGGTATCCCTTTGAATCATTATGTGAAATAGCTGAAA
AGTCAGATCCTGATCAAACATTTAAATTTGCATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAA
GTACCTAATCATGGTTTATGTCACAGCCAGCCTGAGATCATTCTTACGGAAACACCCCAGTACACAACTGAAATAAATAG
ATTGAATTTAGAATCTTCCAATTCAAAGTAGACCTTGAATACAGATTCCCAAGTATCTTCTATTGATTCAGCTGTAATTT
CACCTGATACTGTCCCACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAATAAACCAAAAACTCGTCGAAGT
TTATTAGGAGGACCAACAGCTCTTAGTCCATTCACCCCAAGCTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAGA
TGGATCCTATTTACAAAACTACACTAATACAGCTTCTGAAATTGATGTGCCATCCACCGGAGCCCCTTCAAAAATATCTG
TTGCCAGAATCGGCCAAACTGGAGAAAGTCTGTCTTCTAACAGAGTGGAAATAGCTGAGAGGTAACTCCAACTCTTGCAC
AAGCAGAAAGTTCTGATCCATAAATAAGTACAACCCCTCAGGTATTGGGACCCACTATGACATCTGCCCCAAATGCACTG
CATCGAAGAAGTTCACGACTCTTGACAGTTCCACAACCAAGGTGAATAGGAAGAAATTAAAAATGAAGTTTCCACCTAAA
ATCCCAAACAGAAAAACAAAAAATAAAACTAATAAAGGAGGAATAACTCAACCTAACATAAATGATAGCCTGGAAATTAC
AAAATTGTACTCTTTCATCATTTCAGAAGGGAAAATATCCACAATCACACCTCAGGTACAGGCTTTTAATCTACAAAAAG
CAGCAGCAGAAGGCTTGATAAGCCATCTTCGTGAAAGGGGGAAATGTTATTTAGCTTTGTGTTCATACCACTGCAAAGAA
GCTATAAATATTTTCAGTCATCTACCTTCTCACCACTACAATTCTGGTTGGGTACTGTGCCAAATTGGAAGGGTCTATTT
TGAACTTCCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATATAGTTGAAGACATGG
AAATCTACTCTACAACACTTTAGTATCTTCAAAAAGATGTTGCTCTTTCAGTTCTATCAAAAGACTTAACAGACATGAAT
AAAAATTCACCAGAGGCCTGATGTGCTACAGGGAACAGTTTCAGTCTCCAACGGGAACACGATATTGCAATTAAATTCTT
CCAGGGAGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTCAATCAGGGTGAGAATTTGTCTTAACTGAAGAAT
TGGACAAAACATTAGCTTGTTTTTGAAATGCTATCAGAGTCAATCCTAGACATTGTAATGCATGG

Alignment

ORF - retro_ptro_3288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.06 %
• Parental protein coverage: 77.43 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERL-YAEVHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTP
          M.VLQEPVQAAIWQALNHYAYR...FLA..L.YAEVH.EEALFLLATC.YR.GK.YKAYRLLKG.SC...
Retrocopy MMVLQEPVQAAIWQALNHYAYRVGAFLAKPL<YAEVHTEEALFLLATCSYRPGKDYKAYRLLKGLSCAAL

Parental  QCKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQ
          QCKYLL.KC.VDLSKLAEGEQILSGGVFNK.KSHDDIVTEFGDSACF.L.LLGHVYCKTD.LAKG.ECYQ
Retrocopy QCKYLLEKCYVDLSKLAEGEQILSGGVFNK*KSHDDIVTEFGDSACFPLPLLGHVYCKTDWLAKGLECYQ

Parental  KSLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDT
          KSLSLNPF.W.PFESLCEI.EK.DPDQTFKF.SLQNFSNCLPNSCTTQVPNH.L.H.QPE..LTETPQ.T
Retrocopy KSLSLNPFFWYPFESLCEIAEKSDPDQTFKFASLQNFSNCLPNSCTTQVPNHGLCHSQPEIILTETPQYT

Parental  IELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLT
          .E.NRLNLESSNSK..LNTDS.VS.IDSAVISPDTVPLGTGTSILSKQVQNKPKT.RSLLGGP.ALSP.T
Retrocopy TEINRLNLESSNSK*TLNTDSQVSSIDSAVISPDTVPLGTGTSILSKQVQNKPKTRRSLLGGPTALSPFT

Parental  PSFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQTG-TKSVFSQSGNSREVTPILAQ
          PSFGILPLETPSPGDGSYLQNYTNT.S.IDVPSTGAPSK.SVARIGQTG..KSVF.QSGNS.EVTP.LAQ
Retrocopy PSFGILPLETPSPGDGSYLQNYTNTASEIDVPSTGAPSKISVARIGQTG<RKSVF*QSGNS*EVTPTLAQ

Parental  TQSSGPQTSTTPQVLSPTITSPPNALPRRSSRLFT-SDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGG
          ..SS.P..STTPQVL.PT.TS.PNAL.RRSSRL.T.S..........K...KFP..............GG
Retrocopy AESSDP*ISTTPQVLGPTMTSAPNALHRRSSRLLT<SSTTKVNRKKLKM--KFPXXXXXXXXXXXXXXGG

Parental  ITQPNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINI
          ITQPNINDSLEITKL.S.IISEGKISTITPQ.QAFNLQKAAAEGL.S.LRE.GK.YLALCSY.CKEAINI
Retrocopy ITQPNINDSLEITKLYSFIISEGKISTITPQVQAFNLQKAAAEGLISHLRERGKCYLALCSYHCKEAINI

Parental  LSHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSK
          .SHLPSHHYN.GWVLCQIGR.YFEL.EYMQAERIFSEVRRIENY.VE.MEIYSTTL..LQKDVALSVLSK
Retrocopy FSHLPSHHYNSGWVLCQIGRVYFELPEYMQAERIFSEVRRIENYIVEDMEIYSTTL*YLQKDVALSVLSK

Parental  DLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNA
          DLTDM.KNSPEA.CA.GN.FSLQREHDIAIKFFQ.AIQVDPNYAYAYT..G.EFVLTEELDK.LACF.NA
Retrocopy DLTDMNKNSPEA*CATGNSFSLQREHDIAIKFFQGAIQVDPNYAYAYTQSG*EFVLTEELDKTLACF*NA

Parental  IRVNPRHYNAW
          IRVNPRH.NAW
Retrocopy IRVNPRHCNAW

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	0.11 RPM	79.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3288 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3288 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,