RetrogeneDB ID: retro_ptro_3304

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:7369587..7371498(-)
• 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_3304
ATAACTGTGCTGCAGGAACCCATCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACTGAGATGGAGTTTTCCC
CGCAGAACACCTTTATGCAAAAGTACACTCAGAAGAAGCTTTGTTTTTACTGGTTACCTGTTCTTACCACCCAGGAAAGG
CCTATAAAGCATATAGATTCTTGAAAGGACACAGTTGTCCTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGCTTT
GATGTCAGCAAGCTTGCAGAAGGGGAACAAATCTTACCTGGTGGAGTGTTTCATAAGCAGAAAAGCCATGATGATATTGT
TACTGAGTTTGGTGATTCAGCTTGCTTTACTCTTTCATTGCTGGGACATGCATATTGCAAGACAGATCGGCTTGCCAAAG
GATCAGAGTATGACCAAAACAGCCTTAGTTTAAAGCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGATGAA
AAGCCAGATCCTGACCAAACATTTAAATTTGCATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACA
AGTACCTAATCATAGTTTATGTCACAGACAGCCTGAGACCGTTCTTACGGAAACACCCCAGGACACCACTGAATTAAATA
GATTGAATTTAGAAACTTCCAATTCAAAGTATTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTGTAATT
TCACCTGATACTGTCCCACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAATAAACCAAAAACTTGTTGAAG
TTTGTCAGGAGGACCAGCAGCTCTTAGTCCATTCACCCCAAGCTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAA
ATGGATCCTATTTACAAATCTACACTAATACACCTCTGAAATTGATGTGCCATCCACTGGAGCCCCTTCAGAAAAGTCTG
TCATCAGAAACAGCCAAACTGGAGCAAAGTCTGTCTTCTCGCAGAGTGGAAATAGCCGAGAGGTAACTCCAATTATTGCA
CAAACAGAAAGTTCTGGTCCATAAATAAGTACAACACCTCAGGTATTGAGCCCCACTATGACATCTCCCCCAAATGCACT
CCATTGAAGAAGTTCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGTGAATAGGAAGAAATTAAAAATGAAGTTTC
CACCTAAAATCCCGAACAGAAAAACAAAAAGTAAAACTAATAAGGGAGGAATAACTCAACCTAACATAAATGATAGCCTG
GAAATTACAAAATTGGACTCTTTCATGATTTCAGAAGGGAAAAAAGCCACAATCACACCTCAGATTCAGGCATTAATCTA
AAAGAAGCAGCAACAGAAGGCTTGATGAGCTTTCTTCATGAAAGGGGAAAGGTTATTTAGCTTTGTGTTCATACCACTGC
AAAGAAGCTATAAATATTTTGAGCCATCTACTTTCTCACCACTACAATTCTGGTTGGGTACTGTGCCACATTGGAAGGGT
CTATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGAGTCGAAG
GCATGGAAATCTACTCTACAACACTTTGGCATCTTCAAAAAGATGTTGCTCTTTCAGTTCTGTCAAAAGACTTAACAGAC
ATAGATAAAAATTTACCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACAGGAACACGATATTGCAATTAA
ATTCTTCCAGAGAGCTATCAAAATGGATCCAAATTATGCTTATGCCTATACTCTATCAGGGCGAGAGTTTGTCTTAACTG
AAGAATTGGACAAAGCATTAGCTTGTTTTTGAAATGCTATCAGAGTCAATCCTAGACATTATAATGCATGG

Alignment

ORF - retro_ptro_3304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 77.43 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEVHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          .TVLQEP.QAAIWQALNHYAY.D.VF.AE.LYA.VHSEEALFLL.TC.Y..GKAYKAYR.LKGHSC.TPQ
Retrocopy ITVLQEPIQAAIWQALNHYAY*DGVFPAEHLYAKVHSEEALFLLVTCSYHPGKAYKAYRFLKGHSCPTPQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLLAKCC.D.SKLAEGEQIL.GGVF.KQKSHDDIVTEFGDSACFTLSLLGH.YCKTDRLAKGSE..Q.
Retrocopy CKYLLAKCCFDVSKLAEGEQILPGGVFHKQKSHDDIVTEFGDSACFTLSLLGHAYCKTDRLAKGSEYDQN

Parental  SLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTI
          SLSL.PFLW.PFESLCEI.EKPDPDQTFKF.SLQNFSNCLPNSCTTQVPNHSL.HRQPETVLTETPQDT.
Retrocopy SLSLKPFLWYPFESLCEIDEKPDPDQTFKFASLQNFSNCLPNSCTTQVPNHSLCHRQPETVLTETPQDTT

Parental  ELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTP
          ELNRLNLE.SNSKYSLNTDS.VS.IDSAVISPDTVPLGTGTSILSKQVQNKPKT..SL.GGPAALSP.TP
Retrocopy ELNRLNLETSNSKYSLNTDSPVSSIDSAVISPDTVPLGTGTSILSKQVQNKPKTC*SLSGGPAALSPFTP

Parental  SFGILPLETPSPGDGSYLQNYTNTP-SVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQT
          SFGILPLETPSPG.GSYLQ.YTNTP.S.IDVPSTGAPS.KSV.R..QTG.KSVFSQSGNSREVTPI.AQT
Retrocopy SFGILPLETPSPGNGSYLQIYTNTP<SEIDVPSTGAPSEKSVIRNSQTGAKSVFSQSGNSREVTPIIAQT

Parental  QSSGPQTSTTPQVLSPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGIT
          .SSGP..STTPQVLSPT.TSPPNAL..RSS.LFTSDSSTTK.N.KKLKMKFPPKIPNRKTKSKTNKGGIT
Retrocopy ESSGP*ISTTPQVLSPTMTSPPNALH*RSS*LFTSDSSTTKVNRKKLKMKFPPKIPNRKTKSKTNKGGIT

Parental  QPNINDSLEITKLDSSIISEGKISTITPQIQA-FNLQKAAAEGLMSLLRE-MGKGYLALCSYNCKEAINI
          QPNINDSLEITKLDS..ISEGK..TITPQIQA..NL..AA.EGLMS.L.E..GKGYLALCSY.CKEAINI
Retrocopy QPNINDSLEITKLDSFMISEGKKATITPQIQA<INLKEAATEGLMSFLHE<KGKGYLALCSYHCKEAINI

Parental  LSHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSK
          LSHL.SHHYN.GWVLC.IGR.YFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSK
Retrocopy LSHLLSHHYNSGWVLCHIGRVYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSK

Parental  DLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNA
          DLTD.DKN.PEAWCAAGNCFSLQ.EHDIAIKFFQRAI..DPNYAYAYTL.G.EFVLTEELDKALACF.NA
Retrocopy DLTDIDKNLPEAWCAAGNCFSLQQEHDIAIKFFQRAIKMDPNYAYAYTLSGREFVLTEELDKALACF*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	0.00 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_3304 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3304 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 ,