RetrogeneDB ID: retro_pabe_2094

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:3039193..3041106(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CDC27
• Ensembl ID: ENSPPYG00000008945
• Aliases: None
• Description: cell division cycle 27 [Source:HGNC Symbol;Acc:1728]

Sequence

>retro_pabe_2094
ATGACGGTGCTGCAGGAACCCGTCCAGGCTGCTATACGGCAAGCACTAAACCTCTATGATTACCGAGATGGGGTTTTCAT
TGCAGAACGCCTTTACGCAGAAGTACACTCAGAATAAGCCTTGGTTTTACTGGCGACCTGTTCTTAGCACCCAGGAAAGG
CCTTTAAAGCATATAGACTCTTGAAAGGACACAGTTGTACTACACTGCAATGCAAATACCTGCTTGCAAAATGTTGTGTT
GATCTCAGCAAGCTTGCAGAAGGTGAACAAATCTTATCGGGCAGAGTGTTTCATAAGCAGAAAAGCCATGATGATATTGT
TACTGAGTTTGGTGATTCAGCTTGCTTTCCCCTTCCATTATTGGGACATGTATATTGCAAGACAGATCGACTTGCCAAAG
GATCAGAATGCTACCAAAAGAGCCTTAGTTTAAATCTTTTCTTCTGGTATCCCTTTAAATCATTATGTGAAATAGGTGAA
AAGCCAGATCCTGACCACACATTCTTATTCACATCTTTACAGATCTTTAGCAACTGTCTGCCCAACTCTTGCACAACACA
AGTACCTAATCATAGTTTATGTCACAGACAACCTGAGACCGTTCTTACAGAAACAACCCAGGATACAACTGTATTAAACA
GATTGAATTTATAATCTTCCAATTCAAAATATTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTGTAATT
TCACCTGATACTGTCCCACTGGAAGCAGGAACTTCCATATTTTCTAAACAGGTTCAAAATAAATCAAAAACTGTTCGAAG
TTTATTAGGAGGACCAGCAGCTCTTAGGCCATTAACCCTAAGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAG
ATGGATCCTATTTACAAAACTATACTAACACACCTTCTGAAATTGATGTGCCATCCACCAGAGCCCCTTCAAAAATGTCT
GTTTCCAGAATTGGCCAAACTGGAGCAAAGTCTGTCTTCTCACAGAGGGGAAATAGCCGAGAGGTAACTCCAATTCTTGC
ACAAACAGAAAGTTCTCGTCCATAAATAAATACAACACCTCAGGTTTTGAGCCCCACTATGACATCTCCCCCAAATGCAC
TGCATTGAAGAAGTTCACGACTCTTTACTAGTGACAGTTCCACAACCAAGGAGAATAGGAAGAAATTAAAAATGAATTTT
CCACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACTAATGAAAGAGGAATAACTCAACGTAACATAAATGATAGCCT
GGAAATTACAAAATTGGACTCTTTCATCATTTCAGAAGGGAAAATATCGACAATCACACCTAAGATTCAGGCTTTTAATC
CACAAAAAGCAGCAGCAGAAGGCTTGATGAGCCTTCTTCATGAAAGGGGGAAAGGTTATTTAGCTTTGTGTTCATACCAT
TGCTAAGAAGCTATAAATATTTTGAGCCATCTACCTTCTCACCACTGCAATACTGGTTGGGTACTGTGCCAAATTGGAAG
GGTCTATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGCATTGAGAATTATAGAGTCG
AAGGCATGGAAATCTACTCTACAACACTTTGGCATCTTCAAAAAGATGTTCCTCTTTCAGTTCTGTCAAATGACTTAACA
GACATGGATAAAAATTCGCCAGAGGCCTGGTGTGCTGCAGCGAAGTGTTTCAGTCTGCAATGGGAACACGATATTGCAAT
TAAATTCTTCCAGAGAGCTATCCACGTGGATCCAAATTATGCTTATGCCTATACTCTATTAGGGCAGAAGTTTGTCTTAA
CTGAAGAATTGGACAAAGGATTAGCTTGTTTTTAAATGCTATCAGAGTAAATCCAAGACATTATAATGCATGG

Alignment

ORF - retro_pabe_2094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.32 %
• Parental protein coverage: 77.43 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEXHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          MTVLQEPVQAAI.QALN.Y.YRD.VF.AERLYAE.HSE.AL.LLATC....GKA.KAYRLLKGHSCTT.Q
Retrocopy MTVLQEPVQAAIRQALNLYDYRDGVFIAERLYAEVHSE*ALVLLATCS*HPGKAFKAYRLLKGHSCTTLQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLLAKCCVDLSKLAEGEQILSG.VF.KQKSHDDIVTEFGDSACF.L.LLGHVYCKTDRLAKGSECYQK
Retrocopy CKYLLAKCCVDLSKLAEGEQILSGRVFHKQKSHDDIVTEFGDSACFPLPLLGHVYCKTDRLAKGSECYQK

Parental  SLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTI
          SLSLN.F.W.PF.SLCEIGEKPDPD.TF.FTSLQ.FSNCLPNSCTTQVPNHSL.HRQPETVLTET.QDT.
Retrocopy SLSLNLFFWYPFKSLCEIGEKPDPDHTFLFTSLQIFSNCLPNSCTTQVPNHSLCHRQPETVLTETTQDTT

Parental  ELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTP
          .LNRLNL.SSNSKYSLNTDS.VS.IDSAVISPDTVPL..GTSI.SKQVQNK.KT.RSLLGGPAAL.PLT.
Retrocopy VLNRLNL*SSNSKYSLNTDSPVSSIDSAVISPDTVPLEAGTSIFSKQVQNKSKTVRSLLGGPAALRPLTL

Parental  SFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQTQ
          SFGILPLETPSPGDGSYLQNYTNTPS.IDVPST.APSK.SV.RIGQ.G.KSVFSQ.GNSREVTPILAQT.
Retrocopy SFGILPLETPSPGDGSYLQNYTNTPSEIDVPSTRAPSKMSVSRIGQTGAKSVFSQRGNSREVTPILAQTE

Parental  SSGPQTSTTPQVLSPTITSPTNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQ
          SS.P...TTPQVLSPT.TSP.NAL..RSSRLFTSDSSTTKEN.KKLKM.FPPKIPNRKTKSKTN..GITQ
Retrocopy SSRP*INTTPQVLSPTMTSPPNALH*RSSRLFTSDSSTTKENRKKLKMNFPPKIPNRKTKSKTNERGITQ

Parental  PNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSH
          .NINDSLEITKLDS.IISEGKISTITP.IQAFN.QKAAAEGLMSLL.E.GKGYLALCSY.C.EAINILSH
Retrocopy RNINDSLEITKLDSFIISEGKISTITPKIQAFNPQKAAAEGLMSLLHERGKGYLALCSYHC*EAINILSH

Parental  LPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLT
          LPSHH.NTGWVLCQIGR.YFELSEYMQAERIFSEVR.IENYRVEGMEIYSTTLWHLQKDV.LSVLS.DLT
Retrocopy LPSHHCNTGWVLCQIGRVYFELSEYMQAERIFSEVRSIENYRVEGMEIYSTTLWHLQKDVPLSVLSNDLT

Parental  DMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALAC-FRNAIR
          DMDKNSPEAWCAA..CFSLQ.EHDIAIKFFQRAI.VDPNYAYAYTLLG..FVLTEELDK.LAC.F.NAIR
Retrocopy DMDKNSPEAWCAAAKCFSLQWEHDIAIKFFQRAIHVDPNYAYAYTLLGQKFVLTEELDKGLAC<FLNAIR

Parental  VNPRHYNAW
          VNPRHYNAW
Retrocopy VNPRHYNAW

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	0.06 RPM	43.24 RPM
SRP007412_cerebellum	0.00 RPM	52.05 RPM
SRP007412_heart	0.00 RPM	16.95 RPM
SRP007412_kidney	0.03 RPM	14.25 RPM
SRP007412_liver	0.00 RPM	15.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2094 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2094 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,