RetrogeneDB ID: retro_ptro_3071

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL393516.1:181418..183325(-)
• 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_3071
ATGACGGTGCAGCAGGAACCCGTCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACTGAGTTGGGGTTTTCCT
CGCAGAACACCTTTATGCAGAAGTACACTCAGAAGAAGCCATGTTTTACTGGCGACTTGTTCTTACCACCCAGGAAAGGC
CTATAAAGCATATAGACTCTTGAAAGGACACAGTTGTCTTACACCGCAATGAAAATACCTGCTTGCAAAATGTTGTGTTG
ATCTCAGCAAGCTTGCAGAAGGGGAACAAATCTTATCTGGTGGAGTGTTTAATAGGTAGAAAAGGCATGATGATATTGTT
ACTGAGTTTGGTGATTCAGCTTGCTTTCCCCTTCCATTGTTGGGACATGTACATTGCAAGACAGATCGGCTTGCCAAAGG
ATCAGAATGTGACCAAAAGAGGCTTAGTTTAAAGCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGGTGAAA
GGCCAGATCCTGACCAAACATTTAAATTCACATCTTTTCAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAA
GTACGTAATCATAGTTTATGTCACAGACAGCCTGAGACCTTTCTTGCGGACACACCCCAGGACACAACTGAATTAAACAG
ATTGAATTTAGAATCTTCCAATTCAAAGTATTCCTTGAATACAGATTCCTCAGTGTCTTCTATTGATTCAGCGTAATTTC
ACCTGATACTGTCCAACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAATAAACCAAAAACTGGTCGAAGTT
TTTTAGGAGGACCAGGAGCTCTTAGTCCATTAACCCCAAGTTTTGGGATTTTGCCATTAGGAACCCCAAGTCCTGGAGAT
GGATCCTATTTACAAAACTACACTAATACACCTTCTGAAATTAATGTGCCATCCACCGGAGCCCCTTCAAAAAAGTCTGT
TGCCAGAATCGGACAAACTGGAGCAAAGTCTGTCTTCTCACAGAGTGGAAATAGAAGAGAGGTAACTCCAGTTCTTGCAC
AAACAGAAAGTTCTGGTCCATAAATAAGTACAACACCTCAGGTATTGAGCCCCACTATGACATCTTCCCTAAATGCACTG
CCTTGAAGAAATTCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGAGAATAGGAAGAAATTAAAAAAGAAGTTTCC
ACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACTCAACCTAACATAAATGATAGCCTGG
AAATTACAAAATTGGACTCTTTCATCATTTCAGAAGAGAAAATATCCACAATCACACCTCAGATTCAGGCTTTTAATCAT
AAAAAACAGCAGCAGAAGGCTTGATGAGCCTTCTTCGTGAAAGGGGGAAAGGTTATTTAGCTTTGTGTTCATACCACTGC
AAAGAAGTATAAATATTTTGAGCCATCTACCTTCTCACTACTGCAATACTGGTTGGGTACTGTGCCAAATTGGAAGGGTC
TATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGAGTCGAAGG
CATGGAAATCTACTCTACAACATTTTGGCATCTTCAAAAAGATGTTGCTCTTTCAGTTCTGTCAAAAAACTTAACAGACA
TGGATAAAAATCCGCCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACGGGAACACGATATTGCAATTAAA
TTCTTCCAGGGAGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTCTATTAGGGTGAGAGTTTGTCTTAACTGA
AGAATTGGACAAAGCATTAGCTTGTTTTTGAAATGCTATCAGAGTCAATCCTAGACATTGTAATGCA

Alignment

ORF - retro_ptro_3071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.77 %
• Parental protein coverage: 77.31 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEVHSEEALF-LLATCYYRSGKAYKAYRLLKGHSCTTP
          MTV.QEPVQAAIWQALNHYAY...VFLAE.LYAEVHSEEA.F.LLATC.Y..GKAYKAYRLLKGHSC.TP
Retrocopy MTVQQEPVQAAIWQALNHYAY*VGVFLAEHLYAEVHSEEAMF<LLATCSYHPGKAYKAYRLLKGHSCLTP

Parental  QCKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQ
          Q.KYLLAKCCVDLSKLAEGEQILSGGVFN..K.HDDIVTEFGDSACF.L.LLGHV.CKTDRLAKGSEC.Q
Retrocopy Q*KYLLAKCCVDLSKLAEGEQILSGGVFNR*KRHDDIVTEFGDSACFPLPLLGHVHCKTDRLAKGSECDQ

Parental  KSLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDT
          K.LSL.PFLW.PFESLCEIGE.PDPDQTFKFTS.QNFSNCLPNSCTTQV.NHSL.HRQPET.L..TPQDT
Retrocopy KRLSLKPFLWYPFESLCEIGERPDPDQTFKFTSFQNFSNCLPNSCTTQVRNHSLCHRQPETFLADTPQDT

Parental  IELNRLNLESSNSKYSLNTDSSVSYIDSA-VISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPL
          .ELNRLNLESSNSKYSLNTDSSVS.IDSA.VISPDTV.LGTGTSILSKQVQNKPKTGRS.LGGP.ALSPL
Retrocopy TELNRLNLESSNSKYSLNTDSSVSSIDSA<VISPDTVQLGTGTSILSKQVQNKPKTGRSFLGGPGALSPL

Parental  TPSFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQ
          TPSFGILPL.TPSPGDGSYLQNYTNTPS.I.VPSTGAPSKKSVARIGQTG.KSVFSQSGN.REVTP.LAQ
Retrocopy TPSFGILPLGTPSPGDGSYLQNYTNTPSEINVPSTGAPSKKSVARIGQTGAKSVFSQSGNRREVTPVLAQ

Parental  TQSSGPQTSTTPQVLSPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGI
          T.SSGP..STTPQVLSPT.TS..NALP.R.S.LFTSDSSTTKEN.KKLK.KFPPKIPNRKTKSKTNKGGI
Retrocopy TESSGP*ISTTPQVLSPTMTSSLNALP*RNS*LFTSDSSTTKENRKKLKKKFPPKIPNRKTKSKTNKGGI

Parental  TQPNINDSLEITKLDSSIISEGKISTITPQIQAFNLQ-KAAAEGLMSLLREMGKGYLALCSYNCKE-AIN
          TQPNINDSLEITKLDS.IISE.KISTITPQIQAFN...K.AAEGLMSLLRE.GKGYLALCSY.CKE..IN
Retrocopy TQPNINDSLEITKLDSFIISEEKISTITPQIQAFNHK<KTAAEGLMSLLRERGKGYLALCSYHCKE<SIN

Parental  ILSHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLS
          ILSHLPSH..NTGWVLCQIGR.YFELSEYMQAERIFSEVRRIENYRVEGMEIYSTT.WHLQKDVALSVLS
Retrocopy ILSHLPSHYCNTGWVLCQIGRVYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTFWHLQKDVALSVLS

Parental  KDLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRN
          K.LTDMDKN.PEAWCAAGNCFSLQREHDIAIKFFQ.AIQVDPNYAYAYTLLG.EFVLTEELDKALACF.N
Retrocopy KNLTDMDKNPPEAWCAAGNCFSLQREHDIAIKFFQGAIQVDPNYAYAYTLLG*EFVLTEELDKALACF*N

Parental  AIRVNPRHYNA
          AIRVNPRH.NA
Retrocopy AIRVNPRHCNA

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	0.53 RPM	79.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3071 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3071 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3071 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,