RetrogeneDB ID: retro_pabe_3067

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:60867482..60868851(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP469K1416
• Ensembl ID: ENSPPYG00000015097
• Aliases: None
• Description: ATP-binding cassette sub-family E member 1 [Source:RefSeq peptide;Acc:NP_001126534]

Sequence

>retro_pabe_3067
ATAGCAGACAAATTAATGAGAATTGCATTGTCAACCATGACAAATGTAAACCTAAGAAATGTCAACAGGAATGCAAAAAA
GAGTTGTCCTGTAGTTCAAATGGAAGAATTATGCATAGAAGTTACACCCCAGAGCAAAATAGCATGGATTTCTGAAACTC
TTTGTATTGGTTGTGGTATCTGTATTAAGAAATGCCCTTTCGGCACCTTATCAATTGACAATTTACCAAGCAACTTGGAA
AAAGAAACCACACATTGATATTGTGCCAATGTCTTCAAACTTCACAGGTTGCCTATCCCTCGTCCAGGTAAAGTTTTGGG
ATTAGTTGGAACTAATGATATTGGAAAGTCAACTGCTTTAAAAAATTTTTAGCAGGAAAACAAAAGCCAAACCTTGGAAA
GTAGGATGATCCTCCTGACTGGCAAGAGATTTTGACTTATTTCCGTGGATCTGAATTACAGAATTACTTTACCAAGATTC
TAGAAGAGGACCTAAAAGCCATCATCAAACCTCAATATGTAGAACAGATTCCTAAGCCTGCAAAGGGGACAGTGGGATCT
ATTTTGGACTGAAAAGATGAAACAAAGACACAGGCAATTGCATGTCAGCAGCTTGAATTAACCCACCTAACAGAACAAAA
TGTTGAAGATCTTTCAGGAGGAGAGTTGCAGAGATTTCCCTGTGCTGTCATTTGCATACAGAAAGCTGATATGTTCATGT
TTGATGAGACTTCTAGTTACCTAGATGTCAAGCAGCATTTAAAGCCTGCTATTACTATACAATCTCTGATAAATCCAGAT
AGATATATCATTGTAGTGGAATATGATCTAAGTGTATTAGACTATGTCTCTGACTTCATCTGCTGTTTATATGGTGTACC
AAGCACCTATGGAGTTGTCACTGTGCCTTTTAGTGTAAGAAAGGGCATAAACATTTTTTTGGATGGCTATGTTCCAACAG
AAAACTTGAGATTCAGAGATGCATCACTTGTTTTTAAAGTGGCTGAGACAGCAAATGAAGAAGAAGTCAAAGTGATGTGT
ATGTATAAATATCCAGGAATGAAGAAAAAATGGGAGAGTTTGAGCTAGCAATTGTAGCTGGAGAGTTTACAGATTCTGAA
ATCATGGTGATGATGCTGGGGGAAAATGGAATGGGTAAAACGACATTTATCATAATGCTTGCTGGAAGACTTAAACCTGA
TGAAGAAGGAGAAGTACCAGTTCTAAATGTCAGTTATAAGCTACAGAAAATTAGTCCCAAATCAACTGGAAGTGTTCACC
AGTTACTACATGAAAAGACAAGAGATGCTTATACACATCCACAATTTGTGACTAATGTAATGAAGCCTCTGCAAATTGAA
AACATCATC

Alignment

ORF - retro_pabe_3067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.72 %
• Parental protein coverage: 75.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MADKLTRIA-IVNHDKCKPKKCRQECKK-SCPVVRMGKLCIEVTPQSKIAWISETLCIGCGICIKKCPFG
          .ADKL.RIA.IVNHDKCKPKKC.QECKK.SCPVV.M..LCIEVTPQSKIAWISETLCIGCGICIKKCPFG
Retrocopy IADKLMRIA<IVNHDKCKPKKCQQECKK>SCPVVQMEELCIEVTPQSKIAWISETLCIGCGICIKKCPFG

Parental  ALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTAL-KILAGKQK-PNLGKYDD
          .LSI.NLPSNLEKETTH.YCAN.FKLHRLPIPRPG.VLGLVGTN.IGKSTAL.KI...K.K.PNLGK.DD
Retrocopy TLSIDNLPSNLEKETTH*YCANVFKLHRLPIPRPGKVLGLVGTNDIGKSTAL>KIFSRKTK>PNLGK*DD

Parental  PPDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAVVCQQLDL
          PPDWQEILTYFRGSELQNYFTKILE.DLKAIIKPQYV.QIPK.AKGTVGSILD.KDETKTQA..CQQL.L
Retrocopy PPDWQEILTYFRGSELQNYFTKILEEDLKAIIKPQYVEQIPKPAKGTVGSILD*KDETKTQAIACQQLEL

Parental  THLKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRLKAAITIRSLINPDRYIIVVEHDL
          THL.E.NVEDLSGGELQRF.CAV.CIQKAD.FMFDE.SSYLDVKQ.LK.AITI.SLINPDRYIIVVE.DL
Retrocopy THLTEQNVEDLSGGELQRFPCAVICIQKADMFMFDETSSYLDVKQHLKPAITIQSLINPDRYIIVVEYDL

Parental  SVLDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMC
          SVLDY.SDFICCLYGVPS.YGVVT.PFSVR.GINIFLDGYVPTENLRFRDASLVFKVAETANEEEVK.MC
Retrocopy SVLDYVSDFICCLYGVPSTYGVVTVPFSVRKGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKVMC

Parental  MYKYPGMKK-KMGEFELAIVAGEFTDSEIMV-MLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQ
          MYKYPGMKK.KMGEFELAIVAGEFTDSEIMV.MLGENG.GKTTFI.MLAGRLKPDE.GEVPVLNVSYK.Q
Retrocopy MYKYPGMKK<KMGEFELAIVAGEFTDSEIMVMMLGENGMGKTTFIIMLAGRLKPDEEGEVPVLNVSYKLQ

Parental  KISPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENII
          KISPKSTGSV.QLLHEK.RDAYTHPQFVT.VMKPLQIENII
Retrocopy KISPKSTGSVHQLLHEKTRDAYTHPQFVTNVMKPLQIENII

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	18.80 RPM
SRP007412_cerebellum	0.00 RPM	28.70 RPM
SRP007412_heart	0.00 RPM	23.09 RPM
SRP007412_kidney	0.10 RPM	17.83 RPM
SRP007412_liver	0.03 RPM	20.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3067 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3067 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3067 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3826
Pan troglodytes	retro_ptro_2603

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925, retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067 ,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603,