RetrogeneDB ID: retro_pabe_2184

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b_random:737701..739312(-)
• 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_2184
AGAAAACATGATGATATTGTTACTGAGTTTGGTGATTCAGTTTGCTTTCCCCTTCCATTGTTGGGACGTGTATATTGCAA
GACAGATCAGCTTGCCAAAGGATAAGAATGTTACCAAAAGAGACTTGGTTTAAATCCTTTCCTCTGGTATCCCTTTGAAT
CATTACGTGAAATAGGTGAAAAGCGAGATCCTGACCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTG
CCCAACTCTTGCACAACACAAGTACCTAATCACAGTTTATGTCACAGACAGCCTGAGACCATTCTTATGGAAACACCCCA
GGACACAACTGAATTAAACAGAGTCAATTTAGAATCTTCCAATTCAAAGTACTCCTTGAATACAGATTCCCCTGTGTCTT
TTATTGATTCAGCTGTAATTTCACCTGAAACTATCCCACTGGGAACAGGAAATTCCATATTATCTAAACAGGTTCAAAAT
AAACCAAAAACTGGTCGAAGTTTATTAACAGGACCAGCAGCTCTTAGTCCATTTACCCCAAGTTTTGGGATTTTGCCATT
AGAAACCCCAAGTCCTGGAGATGGATCTTATTTACAAAACTACACTAATACACCTTCTGTAATTGATGTGCCATCCACCG
GAGCCCCTTCAAAAAAGTCTGTTGCCAGAATTGGCCAAACTGGAGCAAAGTCTGTCTTCTCGCAGAATGGAAATGGCCGA
GAGGTAACTCCAATTCTTTCACTAACAGAAATTTCTGGTCCATAAATAACTATAACACCTCAGGTAATGAGCCCCACTAT
GACATCTCCCCCAAATGCACTGCATCAAAGAAGTTCATGACTCTTTACTAGTGACAGTTCGACAACCAAGGAGAATAGGA
AGAAATTAAAAATGAAGTTTCTACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACTCAA
TCTAATATAAATGAAAACCTGGAAATTACAAAATTGGACTCTTCCATCAATTCAGAAGAGGAAATATCCACAATCACACC
TCAGATTCAGGATTTTAATCTACAAAAAGCAGCAGAAGAAGGCTTAATGAGCCTTCTTCATGAAAGTGGGAAACGTTATT
TAGCTTTATGTTCATACCACTGCAAAGAAGCTATAAATATTTTGAGCCATCTACCTTCTCACCACCACAATACTGGTTGG
GTACTGTGCCAAATTGGAAGGTCCTATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAG
GATTGAGAATTATAGATTCGAAGGCATGGAAATCTACTCTAAAACACTTTGGCATCTTCAAAAAATGTCGCTCTTTCATT
TCTATCAAAAGACAACACACATGGATAAAAATTCTCCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACGG
GAACACGATATTGCAATTAAATTCTTCCAGAGAGCTTTCCAAGTGGATCCAAATTATGCTTATGCCTATACTTTATTAGG
GCGAGAGTTTGTCTTAACTGAAGAATTGGACACAGCGTTAGCTTGTTTTTGAAACGCTATCAGAGTCAATCCTAGACATT
ACAATGCATGG

Alignment

ORF - retro_pabe_2184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.87 %
• Parental protein coverage: 65.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQKSLSLNPFLWSPFESLCEIGEKPDPDQTFKF
          ..HDDIVTEFGDS.CF.L.LLG.VYCKTD.LAKG.ECYQK.L.LNPFLW.PFESL.EIGEK.DPDQTFKF
Retrocopy RKHDDIVTEFGDSVCFPLPLLGRVYCKTDQLAKG*ECYQKRLGLNPFLWYPFESLREIGEKRDPDQTFKF

Parental  TSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTIELNRLNLESSNSKYSLNTDSSVSYIDSAVI
          TSLQNFSNCLPNSCTTQVPNHSL.HRQPET.L.ETPQDT.ELNR.NLESSNSKYSLNTDS.VS.IDSAVI
Retrocopy TSLQNFSNCLPNSCTTQVPNHSLCHRQPETILMETPQDTTELNRVNLESSNSKYSLNTDSPVSFIDSAVI

Parental  SPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTPSFGILPLETPSPGDGSYLQNYTNTPSVIDV
          SP.T.PLGTG.SILSKQVQNKPKTGRSLL.GPAALSP.TPSFGILPLETPSPGDGSYLQNYTNTPSVIDV
Retrocopy SPETIPLGTGNSILSKQVQNKPKTGRSLLTGPAALSPFTPSFGILPLETPSPGDGSYLQNYTNTPSVIDV

Parental  PSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQTQSSGPQTSTTPQVLSPTITSPTNALPRRSSR
          PSTGAPSKKSVARIGQ.G.KSVFSQ.GN.REVTPIL..T..SGP....TPQV.SPT.TSP.NAL..RSS.
Retrocopy PSTGAPSKKSVARIGQTGAKSVFSQNGNGREVTPILSLTEISGP*ITITPQVMSPTMTSPPNALHQRSS*

Parental  LFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLDSSIISEGKISTITPQIQ
          LFTSDSSTTKEN.KKLKMKF.PKIPNRKTKSKTNKGGITQ.NIN..LEITKLDSSI.SE..ISTITPQIQ
Retrocopy LFTSDSSTTKENRKKLKMKFLPKIPNRKTKSKTNKGGITQSNINENLEITKLDSSINSEEEISTITPQIQ

Parental  AFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSHLPSHHYNTGWVLCQIGRAYFELSEYMQAER
          .FNLQKAA.EGLMSLL.E.GK.YLALCSY.CKEAINILSHLPSHH.NTGWVLCQIGR.YFELSEYMQAER
Retrocopy DFNLQKAAEEGLMSLLHESGKRYLALCSYHCKEAINILSHLPSHHHNTGWVLCQIGRSYFELSEYMQAER

Parental  IFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFF
          IFSEVRRIENYR.EGMEIYS.TLWHLQK...L.......T.MDKNSPEAWCAAGNCFSLQREHDIAIKFF
Retrocopy IFSEVRRIENYRFEGMEIYSKTLWHLQK-MSLFHFYQKTTHMDKNSPEAWCAAGNCFSLQREHDIAIKFF

Parental  QRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRVNPRHYNAW
          QRA.QVDPNYAYAYTLLG.EFVLTEELD.ALACF.NAIRVNPRHYNAW
Retrocopy QRAFQVDPNYAYAYTLLGREFVLTEELDTALACF*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	0.00 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_2184 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2184 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,