RetrogeneDB ID: retro_ptro_3053

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392524.1:127433..129344(-)
• 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_3053
ATGATAGTGTTACAGGAACCCGTCCAGGCTGCTACATGGCAAGCACTAAACCACTATGCTTACCGAGATGGGGTTTTCCT
CGCAGAACGCCTCTATGCACAAGTACACTCAGAAGAAGCCTTGTTTTTACTGGCGACCTATTCTTACCGCCAGGAAAGGC
CTATAAAGCATATAGACTCTTGAAAGGACACAGTTGTCCTACACCACAATGCAAATACCTGCTTGCAAAATGTTGTTTTG
ATGTCAGCAAGCTTGCAGAAGGGGAACAAATCTTATCTGGTGGAGTGTTTCATAAGCAGAAAAGCCATGATGATATAGTT
ACTGAGTTTGGTGATTCAGCTTGCTTTCCCCTTCCTTTGTTGTGACATGTATATTGCAAGACAGATTGGCTTGCCAAAGG
ATCAGAATGCTACCAAAAGAGCCTTAGTTTAAATCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGGTGAAA
AGCCAGATCCTGACCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGTCCAAGTGTTGCACCATACAA
GTACCTCGTCATAGTTTATGTCACAGACAGCCTGAGACCGTTCTTACGGAAACACCCCAGAACACAACTGAATTAAACAG
ATTGAATTTAGAATCTGCCAATTCAAAGTACTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTGTAATTT
CACCTGATACTCTCCCACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAATAAACCAAAAACTGATCGAAGT
TTATTAGGAGGACCAGCATCTCTTAGTCCATTGACCCCAATTTTTGGTATTTTGCCATTAGAAACCCCAAGTACTGGAGA
TGGATCCTATTTACAAAACTACACTAATACAACTTCTGTAATTGATGTACCATCCACCGGAGTCCCTTCAGAAAATCTGT
TGCCAGAATCGGCTAAACTGGACCAAAGTCTGTCTTCTCACAGAGTGGAAATAGCAGAGAGGTAACTCCAATTCTTGCAC
AAACAGAAAGTTCTGGTCCATAAATAAGTACAACACCTCAGGTATTGAGCCGCACTATGACATATCCCCCAAATGCACTG
CATCAAAGAAGTTCACAACTCTTTACTGGTGACAGTTCCACAACCAAGGAGAATAGGAAAAAATTAAAAATGAATTTTCC
ACCTAAGGTCTCAAACAGAAAAACAAAAAGTAAAACTAGTAAAGGAAGAATAACTCAACCTAATTTAAATGACAGCCTGG
AAATAACAAAATTGGACTCTTCCATCATTTCAGAAGGGAAAATATCCAGAGTCACACCTCAGATTCAGGCTTTTAATCTA
CAAAAAGCAGCAGCAGAAGGCTTTATGAGCCTTCTTCGTGAAAGGGGGAAAGTTTATTTAGCTTTGTGTTCATACCACTG
CAAAGAAGCTATAAATATTTTGAACCATTTACCTTCTCACCACTACAATACTGGTTGGGTACTGTGCCAAATTGGAAGGG
CCTATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCACAAGTTAGAAGGATTGAGAATTATAGAGTCCAA
GGCATGGAAATCTACTCTACAACACTTTGGCATCTTCAAAAAGATGTTTCTCTTTCATTTCTGTCAACAGACTTAACAGA
CAGGGATAAAAATTTGCCAGAGCCTGGTGTGCTGCAGGGAACTGTTTCACTCTGCAACGGGAACACGATATTGCAATTAA
ATTCTTCCAGAGAGCTATCCAAGTGGATCCAAATTATGCTTATGTCGATACTCTATTAGGGCATGAGTTTGTCTTAACTG
AAGAATTGGACAAAGCATTAGCTAGTTTTTGAAATGCTATCAGAGTCAATCCTAGACATTATAATGCATGG

Alignment

ORF - retro_ptro_3053 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.14 %
• Parental protein coverage: 77.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEVHSEEALFLLATCYYRS-GKAYKAYRLLKGHSCTTP
          M.VLQEPVQAA.WQALNHYAYRD.VFLAERLYA.VHSEEALFLLAT..YR..GKAYKAYRLLKGHSC.TP
Retrocopy MIVLQEPVQAATWQALNHYAYRDGVFLAERLYAQVHSEEALFLLATYSYRQ<GKAYKAYRLLKGHSCPTP

Parental  QCKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQ
          QCKYLLAKCC.D.SKLAEGEQILSGGVF.KQKSHDDIVTEFGDSACF.L.LL.HVYCKTD.LAKGSECYQ
Retrocopy QCKYLLAKCCFDVSKLAEGEQILSGGVFHKQKSHDDIVTEFGDSACFPLPLL*HVYCKTDWLAKGSECYQ

Parental  KSLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDT
          KSLSLNPFLW.PFESLCEIGEKPDPDQTFKFTSLQNFSNCL...CT.QVP.HSL.HRQPETVLTETPQ.T
Retrocopy KSLSLNPFLWYPFESLCEIGEKPDPDQTFKFTSLQNFSNCLSKCCTIQVPRHSLCHRQPETVLTETPQNT

Parental  IELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLT
          .ELNRLNLES.NSKYSLNTDS.VS.IDSAVISPDT.PLGTGTSILSKQVQNKPKT.RSLLGGPA.LSPLT
Retrocopy TELNRLNLESANSKYSLNTDSPVSSIDSAVISPDTLPLGTGTSILSKQVQNKPKTDRSLLGGPASLSPLT

Parental  PSFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPS-KKSVARIGQTGTKSVFSQSGNSREVTPILAQ
          P.FGILPLETPS.GDGSYLQNYTNT.SVIDVPSTG.PS..KSVARIG.TG.KSVFSQSGNSREVTPILAQ
Retrocopy PIFGILPLETPSTGDGSYLQNYTNTTSVIDVPSTGVPS<RKSVARIG*TGPKSVFSQSGNSREVTPILAQ

Parental  TQSSGPQTSTTPQVLSPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGI
          T.SSGP..STTPQVLS.T.T.PPNAL..RSS.LFT.DSSTTKEN.KKLKM.FPPK..NRKTKSKT.KG.I
Retrocopy TESSGP*ISTTPQVLSRTMTYPPNALHQRSSQLFTGDSSTTKENRKKLKMNFPPKVSNRKTKSKTSKGRI

Parental  TQPNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINIL
          TQPN.NDSLEITKLDSSIISEGKIS..TPQIQAFNLQKAAAEG.MSLLRE.GK.YLALCSY.CKEAINIL
Retrocopy TQPNLNDSLEITKLDSSIISEGKISRVTPQIQAFNLQKAAAEGFMSLLRERGKVYLALCSYHCKEAINIL

Parental  SHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKD
          .HLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFS.VRRIENYRV.GMEIYSTTLWHLQKDV.LS.LS.D
Retrocopy NHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSQVRRIENYRVQGMEIYSTTLWHLQKDVSLSFLSTD

Parental  LTDMDKNSPE-AWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNA
          LTD.DKN.PE.AWCAAGNCF.LQREHDIAIKFFQRAIQVDPNYAY..TLLGHEFVLTEELDKALA.F.NA
Retrocopy LTDRDKNLPE<AWCAAGNCFTLQREHDIAIKFFQRAIQVDPNYAYVDTLLGHEFVLTEELDKALASF*NA

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	0.04 RPM	31.05 RPM
SRP007412_cerebellum	0.43 RPM	34.49 RPM
SRP007412_heart	0.41 RPM	34.54 RPM
SRP007412_kidney	0.34 RPM	25.21 RPM
SRP007412_liver	0.13 RPM	17.94 RPM
SRP007412_testis	3.16 RPM	79.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3053 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3053 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3053 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,