RetrogeneDB ID: retro_pabe_2178

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b_random:12073557..12075469(+)
• 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_2178
ATGACGGTGCTGCAGGAACCCGTCCAGACTGATATATGGCAAGCACTAAACCACTATGCTTGCTGAGATGGGGTTTTCCT
CGCAGAATATCTTTATGCAGAAATACACTCAGAAGAAGCCTCGTTTTTACTGGCGACCTGTTCTTACTGCCCAGGAAAGG
CTTATAAAGCATATAGACTCTTGAAAGGACACAGTTGTCCTACAACACAATGCAAATACCTGCTTACAAAATGTTGTGTT
GATCTCAGCAAGTTTGCAGAAGGGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGTAGAAAAGCCATGATGATATTGT
TACTGATTTTGGTGATTCAGCTTGCTTTCCTCTTCCATTGTTAGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAG
GATCAGAATGTTACCAAAAGAGCCTTAGTTTAAATCCTTTCTTCTGCTATGCCTTTGAATCATTATGTGTAATAGGTGAA
AAGCCAGATCCGACCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAA
GTACCTAATCATAGTTTATGTCACAGACAGCCTGAGACCTTTCTTATGGAAACACCCCAGGACACAATTGAATTAAACAG
ATTGAATTTAGAATCTTCCAATTCAAAGTATTCCTTGAATACAGATTCCCCTGTGTCTTCTATTGATTCAGATGTAATTT
CACCTGATACTGTCCCACTGGGAAGAGGAACTTCCATATTATCTAAACAGGTTTAAAATAAACCAAAAACAGGTCAAAGT
TTATTAGGAGGAGCAGCAGCTCTTAGTCCATTCACCCCAAGTTTTGGTATTTTGCCATTAGAAACCCCAAGTCCTGGAGA
TGGAGCCTATTTACAAAATTACACTAATACACCTTCTGAAATTGATGTGCCATCCACCGGAGCCCCTTCAAAAAAGTCTG
TTGCCAGAATCGGCCAAACTGGAGAAAAGTCTATCTTCTCACAGAGTGGAAATAGCCAAGAGGTAACTCCAATTCTTGCA
CAAACAGAAAGTTCTGGTCCATAAATAGGTACAACACCTCAGGTATTGAGCCCCACTATGACATCTCCCACAAATGTACT
GCATCAAAAGGTGCATGACTCTTTACTAGTGACAGTTCCAAAACCAAGGCAAATAGGAAGAAATTAAAAATGAAGTTTCC
ACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACTCAACCTAACATAAATGATAGCTTGG
AAATTACAAAATTGGACTCTTTCATCATTTCAGAAGGGAAAATATCCACAATCACACCTCAGATTCAGGCTTTTAATCCA
CAAAAAGCAGCAGCAGAAGGCTTGATGAGCCTTCCTCATGAAAGGGGGAAAGGTTATTTAGCTTTGTGGTCATACCATTA
CAAGGGAGCTATAAATATTTTGAGCCATCTACCTTCTCACCACTACAATACTGGTTGGATACTGTGCCAAATTGGAAGGG
TCTATTTTGAACTTTCAGAGTACATGCAAGCTGATAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGAGTCGAA
GGCATGGAAATCTACTGTACAACACTTTGGCATCTTCTAAAAGATGTCGCTCTTACAGTTCTGTCAAAAGACTTAACAGA
CATGGATAAAAATTCGCCAGAGGCCTGATGTGCTGCAGGGAAGTGTTTCAGTCTGCAATGGGAACACGATATTGCAATTA
AATTCTTCCAGAGAGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTGTATTAGGGCGAGAGTTTGTCTTAACT
GAAGAATTGGACAAAGCATTAGCTTGTTTGTGAAATGCTATCAGAGTCAATCCTAGACATTGTAATGCATGG

Alignment

ORF - retro_pabe_2178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 77.43 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEXHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          MTVLQEPVQ..IWQALNHYA..D.VFLAE.LYAE.HSEEA.FLLATC.Y..GKAYKAYRLLKGHSC.T.Q
Retrocopy MTVLQEPVQTDIWQALNHYAC*DGVFLAEYLYAEIHSEEASFLLATCSYCPGKAYKAYRLLKGHSCPTTQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLL.KCCVDLSK.AEGEQILSGGVFNK.KSHDDIVT.FGDSACF.L.LLGHVYCKTDRLAKGSECYQK
Retrocopy CKYLLTKCCVDLSKFAEGEQILSGGVFNK*KSHDDIVTDFGDSACFPLPLLGHVYCKTDRLAKGSECYQK

Parental  SLSLNPFLWSPFESLCEIGEKPDP-DQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDT
          SLSLNPF....FESLC.IGEKPDP.DQTFKFTSLQNFSNCLPNSCTTQVPNHSL.HRQPET.L.ETPQDT
Retrocopy SLSLNPFFCYAFESLCVIGEKPDP<DQTFKFTSLQNFSNCLPNSCTTQVPNHSLCHRQPETFLMETPQDT

Parental  IELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLT
          IELNRLNLESSNSKYSLNTDS.VS.IDS.VISPDTVPLG.GTSILSKQV.NKPKTG.SLLGG.AALSP.T
Retrocopy IELNRLNLESSNSKYSLNTDSPVSSIDSDVISPDTVPLGRGTSILSKQV*NKPKTGQSLLGGAAALSPFT

Parental  PSFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQT
          PSFGILPLETPSPGDG.YLQNYTNTPS.IDVPSTGAPSKKSVARIGQ.G.KS.FSQSGNS.EVTPILAQT
Retrocopy PSFGILPLETPSPGDGAYLQNYTNTPSEIDVPSTGAPSKKSVARIGQTGEKSIFSQSGNSQEVTPILAQT

Parental  QSSGPQTSTTPQVLSPTITSPTNALPRR-SSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGI
          .SSGP...TTPQVLSPT.TSPTN.L.......LFTSDSS.TK.N.K...................NKGGI
Retrocopy ESSGP*IGTTPQVLSPTMTSPTNVLHQK<GA*LFTSDSSKTKANRKXXXXXXXXXXXXXXXXXXXNKGGI

Parental  TQPNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINIL
          TQPNINDSLEITKLDS.IISEGKISTITPQIQAFN.QKAAAEGLMSL..E.GKGYLAL.SY..K.AINIL
Retrocopy TQPNINDSLEITKLDSFIISEGKISTITPQIQAFNPQKAAAEGLMSLPHERGKGYLALWSYHYKGAINIL

Parental  SHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKD
          SHLPSHHYNTGW.LCQIGR.YFELSEYMQA.RIFSEVRRIENYRVEGMEIY.TTLWHL.KDVAL.VLSKD
Retrocopy SHLPSHHYNTGWILCQIGRVYFELSEYMQADRIFSEVRRIENYRVEGMEIYCTTLWHLLKDVALTVLSKD

Parental  LTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAI
          LTDMDKNSPEA.CAAG.CFSLQ.EHDIAIKFFQRAIQVDPNYAYAYT.LG.EFVLTEELDKALAC..NAI
Retrocopy LTDMDKNSPEA*CAAGKCFSLQWEHDIAIKFFQRAIQVDPNYAYAYTVLGREFVLTEELDKALACL*NAI

Parental  RVNPRHYNAW
          RVNPRH.NAW
Retrocopy RVNPRHCNAW

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	0.00 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_2178 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2178 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,