RetrogeneDB ID: retro_pabe_2172

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b_random:993812..995631(+)
• 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_2172
TACCAAGNNNNNNNNNNAGAAGAAGCCTTGTTTTTAATGGCGACCTGTTCTTACCTCCCAGGAAAGTCCTATAAAGCATA
TAGACTCTTGAAAAGACATAGTTGTCCTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGTAAGC
TTGCAGACTGGGAGCAAATCTTATCTGGTGGAGTGTTTAATAAGAAGAAAAGCCATGATGATATTGTTACTGAGTTTGGT
GATTCAGTTTGCTTTCCCCTTCCATTGTTGGGACGTGTATATTGCAAGACAGATCGGCTTGCTAAAGGATAAGAATGTTA
CCAAAAGAGACTTAGTTTAAATCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTG
GCCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGTACAACACAAGTACCTAATCAC
AGTTTATGTCACAGACAGCCTGAGACCATTCTTATGGAAACACCCCAGGACACAACTGAATTAAACAGAGTCAGTTTAGA
ATCTTCCAATTCAAAGTACTCCTTGAATACAGATTCCCCAGTGTCTTTTATTGATTCAGCTGTAATTTCACCTGAAACTG
TCCCACTGGGAACAGAAACTTCCATGTTATCTAAACAGGTTAAAAATAAACCAAAAACTGGTCGAAGTTTATTAACAGGA
CCAGCAGCTCTTAGTCCATTTACTCCAAGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAGATGGATCTTATTT
ACAAACTACACTAATACACCTTCTGTAATTGATGTGCCATCCACCGGAGCCCCTTCAATAAAGTCTGTTGCCAGAATTGG
CCAAACTGGAGCAAAGTCTGTCTTCTCGCAGAGTGGAAATAGCCGAGAGGTAACTCCAATTCTTTCACTAACATAAAGTT
CTGGTCCATAAATAACTACAACACCTCAGGTAATGAGCCCCACTATGACAACTCCCCCAAATGCACTGCATCGAAGAAGT
TCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGAGAATAAGAAGAAATTAAAAATGAAGTTTCCACCTGAAATCCT
AAAGAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACCCAATCTAATATAAATGAAAACCTGGAAATTACAAAAT
TGGACTCTTCCATCAATTCAGAAGAGGAAATATCCACAATCACACCTCAGATTCAGGCTTTTAATCTACAAAAAGCAGCA
GCAGAAGGCTTGATGAGCCTTCTTCATGAAAGCAGGAAAGGTTATTTAGCTTTATGTTCATACCACTGCAAAGAAGCTAT
AAATATTTTGAGCCATCTACCTTCTCACCACTACAATATTGGTTGGGAACTGTGCCAAATTGGAAGGTCCTATTTTGAAC
TTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGATTCGAAGGCATGGAAATC
TACTCTACAACACTTTGGCATCTTCAAAAAGATGTCGCTCTTTCATTTCTGTCAAAAGACTTAACAGACATGGATAAAAA
TTCTCCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACAGGACACGATATTGCAATTAAATTCTCCCAGAG
AGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTTTATTAGGGCGAGAGTTTGTCTTAATTGAAGAATTGGACA
AAGCGTTAGCTTGTTTTTGAAATGCTATCAGAGTCAATCCTAGACATTACAATGCATGG

Alignment

ORF - retro_pabe_2172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.19 %
• Parental protein coverage: 73.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YAEXHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQCKYLLAKCCVDLSKLAEGEQILSGGVFNKQK
          Y..X..EEALFL.ATC.Y..GK.YKAYRLLK.HSC.TPQCKYLLAKCCVDLSKLA..EQILSGGVFNK.K
Retrocopy YQXXXXEEALFLMATCSYLPGKSYKAYRLLKRHSCPTPQCKYLLAKCCVDLSKLADWEQILSGGVFNKKK

Parental  SHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQKSLSLNPFLWSPFESLCEIGEKPDPDQTFKFT
          SHDDIVTEFGDS.CF.L.LLG.VYCKTDRLAKG.ECYQK.LSLNPFLW.PFESLCEIGEKPDP.QTFKFT
Retrocopy SHDDIVTEFGDSVCFPLPLLGRVYCKTDRLAKG*ECYQKRLSLNPFLWYPFESLCEIGEKPDPGQTFKFT

Parental  SLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTIELNRLNLESSNSKYSLNTDSSVSYIDSAVIS
          SLQNFSNCLPNSCTTQVPNHSL.HRQPET.L.ETPQDT.ELNR..LESSNSKYSLNTDS.VS.IDSAVIS
Retrocopy SLQNFSNCLPNSCTTQVPNHSLCHRQPETILMETPQDTTELNRVSLESSNSKYSLNTDSPVSFIDSAVIS

Parental  PDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTPSFGILPLETPSPGDGSYLQ-NYTNTPSVIDV
          P.TVPLGT.TS.LSKQV.NKPKTGRSLL.GPAALSP.TPSFGILPLETPSPGDGSYLQ.NYTNTPSVIDV
Retrocopy PETVPLGTETSMLSKQVKNKPKTGRSLLTGPAALSPFTPSFGILPLETPSPGDGSYLQ<NYTNTPSVIDV

Parental  PSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQTQSSGPQTSTTPQVLSPTITSPTNALPRRSSR
          PSTGAPS.KSVARIGQ.G.KSVFSQSGNSREVTPIL..T.SSGP...TTPQV.SPT.T.P.NAL.RRSS.
Retrocopy PSTGAPSIKSVARIGQTGAKSVFSQSGNSREVTPILSLT*SSGP*ITTTPQVMSPTMTTPPNALHRRSS*

Parental  LFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLDSSIISEGKISTITPQIQ
          LFTSDSSTTKEN.KKLKMKFPP.I..RKTKSKTNKGGITQ.NIN..LEITKLDSSI.SE..ISTITPQIQ
Retrocopy LFTSDSSTTKENKKKLKMKFPPEILKRKTKSKTNKGGITQSNINENLEITKLDSSINSEEEISTITPQIQ

Parental  AFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSHLPSHHYNTGWVLCQIGRAYFELSEYMQAER
          AFNLQKAAAEGLMSLL.E..KGYLALCSY.CKEAINILSHLPSHHYN.GW.LCQIGR.YFELSEYMQAER
Retrocopy AFNLQKAAAEGLMSLLHESRKGYLALCSYHCKEAINILSHLPSHHYNIGWELCQIGRSYFELSEYMQAER

Parental  IFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTDMDKNSPEAWCAAGNCFSLQRE-HDIAIKF
          IFSEVRRIENYR.EGMEIYSTTLWHLQKDVALS.LSKDLTDMDKNSPEAWCAAGNCFSLQ...HDIAIKF
Retrocopy IFSEVRRIENYRFEGMEIYSTTLWHLQKDVALSFLSKDLTDMDKNSPEAWCAAGNCFSLQQD<HDIAIKF

Parental  FQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRVNPRHYNAW
          .QRAIQVDPNYAYAYTLLG.EFVL.EELDKALACF.NAIRVNPRHYNAW
Retrocopy SQRAIQVDPNYAYAYTLLGREFVLIEELDKALACF*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_2172 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2172 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,