RetrogeneDB ID: retro_pabe_3556

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:71383871..71385533(+)
• 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_3556
ATGACAGTGCTGCAGGAACCCGTCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGGGGTTTTCCT
CACAGAACGCCTTTATGCAGAAGTACACTCAGAAGAAGCCTTGTTTTTAATGGCGACCTGTTCTTACCTCCCAGGAAAGG
CCTATAAAGCATATAGACTCTTGCAAAGACACAGTTGTCCTACACCACAATGCAAATACCTGCTTGCAAAATGTTGTGTT
GATCTCAGTAAGCTTGCAGACTGGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGT
TACTGAGTTTGGTGATTCAGTTTGCTTTCCCCTTCCATTGTTGGGACGTGTATATTGCAAGACAGATCGGCTTGCTAAAG
GATAAGAATGTTACCAAAAAAGACTTAGTTTAAATCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGGTGAA
AAGCCAGATCCTGACCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACA
AGTACCTAATCACAGTTTATGTCACAGACAGCCTGAGACCATTCTTATGGAAACACCCCAGGACACAACTGAATTAAACA
GAGTCAATTTAGAATCTTCCAATTCAAAGTACTCCTTGAATACAGATTCCCCAGTGTCTTTTATTGATTCAGCTGTAATT
TCACCTGAAACTGTCCCACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAGTAAACCAAAAACTGGTCGAAG
TTTATTAACAGGACCAACAGCTCTTAGTCCATTTACCCCAAGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAG
ATGGATCTTATTTATAAAACTACACTAATACACCTTCTGTAATTGATGTGCCATCCACCGGTGCCCCTTCAAAAAAGTCT
GTTGCCAGAATTGGCCAAACTGGATCAAAGTCTATCTTCTCGCAGAGTGGAAATAGCCGAGAGGTAACTCCAATTCTTTC
ACTAACAGAAAGTTCTGGTCCATAAATAACTACAACACCTCAGGTAATGAGCCCCTCTATGACACCTCCCCCAAATGCAC
TGCATCGAAGAAGTTCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGAGAATAGGAAGAAATTAAAAATGAAGTTT
CCACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACTCAATCTAATATAAATGACAACCT
GGAAATTACAAAATTGGACTCTTCCATCAATTCAGAAGAGGAAATATCCACAATCACACCTCAGATTCAGGCTTTTAATC
TACAAAAAGCAGCAGCAGAAGGCTTGATGAGCCTTCTTCATGAAAGGGGGAAAGTTTATTTAGCTTTATGTTCATACCAC
TGCAAAGAAGCTATAAATATTTTGAGCCATCTACGTTCTCACCACTACAATACTGGTTGGGTACTGTGCCAAATTGGAAG
GTCCTATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGATTCG
AAGGCATGGAAATTTACAACACTTTGGCATATTCAAAAAGATGTCACTCTTTCCTTTCTGTC

Alignment

ORF - retro_pabe_3556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87. %
• Parental protein coverage: 67.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEXHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          MTVLQEPVQAAIWQALNHYAYRD.VFL.ERLYAE.HSEEALFL.ATC.Y..GKAYKAYRLL..HSC.TPQ
Retrocopy MTVLQEPVQAAIWQALNHYAYRDGVFLTERLYAEVHSEEALFLMATCSYLPGKAYKAYRLLQRHSCPTPQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLLAKCCVDLSKLA..EQILSGGVFNKQKSHDDIVTEFGDS.CF.L.LLG.VYCKTDRLAKG.ECYQK
Retrocopy CKYLLAKCCVDLSKLADWEQILSGGVFNKQKSHDDIVTEFGDSVCFPLPLLGRVYCKTDRLAKG*ECYQK

Parental  SLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTI
          .LSLNPFLW.PFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSL.HRQPET.L.ETPQDT.
Retrocopy RLSLNPFLWYPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLCHRQPETILMETPQDTT

Parental  ELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTP
          ELNR.NLESSNSKYSLNTDS.VS.IDSAVISP.TVPLGTGTSILSKQVQ.KPKTGRSLL.GP.ALSP.TP
Retrocopy ELNRVNLESSNSKYSLNTDSPVSFIDSAVISPETVPLGTGTSILSKQVQSKPKTGRSLLTGPTALSPFTP

Parental  SFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQTQ
          SFGILPLETPSPGDGSYL.NYTNTPSVIDVPSTGAPSKKSVARIGQ.G.KS.FSQSGNSREVTPIL..T.
Retrocopy SFGILPLETPSPGDGSYL*NYTNTPSVIDVPSTGAPSKKSVARIGQTGSKSIFSQSGNSREVTPILSLTE

Parental  SSGPQTSTTPQVLSPTITSPTNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQ
          SSGP...TTPQV.SP..T.P.NAL.RRSS.LFTSDSSTTKEN.KKLKMKFPPKIPNRKTKSKTNKGGITQ
Retrocopy SSGP*ITTTPQVMSPSMTPPPNALHRRSS*LFTSDSSTTKENRKKLKMKFPPKIPNRKTKSKTNKGGITQ

Parental  PNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSH
          .NIND.LEITKLDSSI.SE..ISTITPQIQAFNLQKAAAEGLMSLL.E.GK.YLALCSY.CKEAINILSH
Retrocopy SNINDNLEITKLDSSINSEEEISTITPQIQAFNLQKAAAEGLMSLLHERGKVYLALCSYHCKEAINILSH

Parental  LPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSV
          L.SHHYNTGWVLCQIGR.YFELSEYMQAERIFSEVRRIENYR.EGMEIY.T..........LSV
Retrocopy LRSHHYNTGWVLCQIGRSYFELSEYMQAERIFSEVRRIENYRFEGMEIYNTLAYSKRCHSFLSV

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_3556 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3556 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,