RetrogeneDB ID: retro_ptro_2972

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL389469.1:1448..3107(+)
• 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_2972
CTTGCAGAAGGGGAACAAATCTTACCTTTTGGAGTGTTTCATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGG
TGATTCAGCTTGCTTTACTCTTTCATTGCTGGGACATGCATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAGTATG
ACCAAAACAGCCTTAGTTTAAAGCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGATGAAAAGCCAGATCCT
GACCAAACATTTAAATTTGCATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCA
TAGTTTATGTCACAGACAGCCTGAGACCGTTCTTACGGAAACACCCCAGGACACCACTGAATTAAATAGATTGAATTTAG
AAACTTCCAATTCAAAGTATTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTGTAATTTCACCTGATACT
GTCCCACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAATAAACCAAAAACTTGTTGAAGTTTGTCAGGAGG
ACCAGCAGCTCTTAGTCCATTCACCCCAAGCTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAAATGGATCCTATT
TACAAATCTACACTAATACACCTCTGAAATTGATGTGCCATCCACTGGAGCCCCTTCAGAAAAGTCTGTCATCAGAAACA
GCCAAACTGGAGCAAAGTCTGTCTTCTCGCAGAGTGGAAATAGCCGAGAGGTAACTCCAATTATTGCACAAACAGAAAGT
TCTGGTCCATAAATAAGTACAACACCTCAGGTATTGAGCCCCACTATGACATCTCCCCCAAATGCACTCCATTGAAGAAG
TTCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGTGAATAGGAAGAAATTAAAAATGAAGTTTCCACCTAAAATCC
CGAACAGAAAAACAAAAAGTAAAACTAATAAGGGAGGAATAACTCAACCTAACATAAATGATAGCCTGGAAATTACAAAA
TTGGACTCTTTCATGATTTCAGAAGGGAAAAAAGCCACAATCACACCTCAGATTCAGGCATTAATCTAAAAGAAGCAGCA
ACAGAAGGCTTGATGAGCTTTCTTCATGAAAGGGGAAAGGTTATTTAGCTTTGTGTTCATACCACTGCAAAGAAGCTATA
AATATTTTGAGCCATCTACTTTCTCACCACTACAATTCTGGTTGGGTACTGTGCCACATTGGAAGGGTCTATTTTGAACT
TTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGAGTCGAAGGCATGGAAATCT
ACTCTACAACACTTTGGCATCTTCAAAAAGATGTTGCTCTTTCAGTTCTGTCAAAAGACTTAACAGACATAGATAAAAAT
TTACCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACAGGAACACGATATTGCAATTAAATTCTTCCAGAG
AGCTATCAAAATGGATCCAAATTATGCTTATGCCTATACTCTATCAGGGCGAGAGTTTGTCTTAACTGAAGAATTGGACA
AAGCATTAGCTTGTTTTTGAAATGCTATCAGAGTCAATCCTAGACATTATAATGCATGG

Alignment

ORF - retro_ptro_2972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 67.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQKSLSLNPFLWSPFES
          LAEGEQIL..GVF.KQKSHDDIVTEFGDSACFTLSLLGH.YCKTDRLAKGSE..Q.SLSL.PFLW.PFES
Retrocopy LAEGEQILPFGVFHKQKSHDDIVTEFGDSACFTLSLLGHAYCKTDRLAKGSEYDQNSLSLKPFLWYPFES

Parental  LCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTIELNRLNLESSNSKY
          LCEI.EKPDPDQTFKF.SLQNFSNCLPNSCTTQVPNHSL.HRQPETVLTETPQDT.ELNRLNLE.SNSKY
Retrocopy LCEIDEKPDPDQTFKFASLQNFSNCLPNSCTTQVPNHSLCHRQPETVLTETPQDTTELNRLNLETSNSKY

Parental  SLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTPSFGILPLETPSPGD
          SLNTDS.VS.IDSAVISPDTVPLGTGTSILSKQVQNKPKT..SL.GGPAALSP.TPSFGILPLETPSPG.
Retrocopy SLNTDSPVSSIDSAVISPDTVPLGTGTSILSKQVQNKPKTC*SLSGGPAALSPFTPSFGILPLETPSPGN

Parental  GSYLQNYTNTP-SVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQTQSSGPQTSTTPQVL
          GSYLQ.YTNTP.S.IDVPSTGAPS.KSV.R..QTG.KSVFSQSGNSREVTPI.AQT.SSGP..STTPQVL
Retrocopy GSYLQIYTNTP<SEIDVPSTGAPSEKSVIRNSQTGAKSVFSQSGNSREVTPIIAQTESSGP*ISTTPQVL

Parental  SPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLD
          SPT.TSPPNAL..RSS.LFTSDSSTTK.N.KKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLD
Retrocopy SPTMTSPPNALH*RSS*LFTSDSSTTKVNRKKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLD

Parental  SSIISEGKISTITPQIQA-FNLQKAAAEGLMSLLRE-MGKGYLALCSYNCKEAINILSHLPSHHYNTGWV
          S..ISEGK..TITPQIQA..NL..AA.EGLMS.L.E..GKGYLALCSY.CKEAINILSHL.SHHYN.GWV
Retrocopy SFMISEGKKATITPQIQA<INLKEAATEGLMSFLHE<KGKGYLALCSYHCKEAINILSHLLSHHYNSGWV

Parental  LCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTDMDKNSPEAWC
          LC.IGR.YFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTD.DKN.PEAWC
Retrocopy LCHIGRVYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTDIDKNLPEAWC

Parental  AAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRVNPRHYNAW
          AAGNCFSLQ.EHDIAIKFFQRAI..DPNYAYAYTL.G.EFVLTEELDKALACF.NAIRVNPRHYNAW
Retrocopy AAGNCFSLQQEHDIAIKFFQRAIKMDPNYAYAYTLSGREFVLTEELDKALACF*NAIRVNPRHYNAW

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	0.02 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_2972 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2972 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,