RetrogeneDB ID: retro_pabe_3518

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9_random:9992126..9993495(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP4
• Ensembl ID: ENSPPYG00000004149
• Aliases: None
• Description: FK506 binding protein 4, 59kDa [Source:HGNC Symbol;Acc:3720]

Sequence

>retro_pabe_3518
ATGACAGCCAAGGAGATGAAGGCGACCGAGAGTGCGGCGCAGCCGGAGCCGCTGCCCAAGAAGGAAGTGGAAGTCAGCCC
CAAACAGGATGAAGGAGTGCTGAAGGTCATCAAGAGAGAGGGCACAGGTACAGAGATGCCCATGACTGGGGACCTAGTCT
TTGTCCACTACACTGGCTGGCTGTTAGAGGGCACAAAGTTTGACTCCAGTGTGGGTGGCAAGGACAGACTCTCCTTTGAC
CTGGGAAAAGGGGAGGTCATCAAGGCTTGGGACATTGCCGTAGCAATCATGAAGGTGGGGGAGGTGTGCCACATCACCTG
CAAACCAGAATATGCCTAGGGTTCAGTAGGCAGTCCTCCAACGGTCCCCCCATAATGCCACGCTTGTGTTTGAGGTGGAA
TTGTTTAAGGAAGAAGATCTGACGGAAGAGGAAGATGGGGGAATCGTCCGCAGAATAGGGACTCGCGGTGAAGGCTATGT
CAAGCCCGATGAGGGCACTATGTTGGAGGTTGCGCTGAAAGGGTGCTGCAAGGACCAGCTCTTTGACCAACGGGCGCTCC
GCTTTGAGGTTAGCGTGGGGGAGAACCTGGATCTGCCTTATGATCTGGAGAGGGCCATTCAGCACTTGGAGAAAGGAGAA
CATTCCACTGTGTACCTCAGGCCCAGCTATGCTTTTGGCAGTGTTGGGAAGGAAAAGTTCCAAATCCCATCAAATGCCGA
GCTGAAATATGAATTACACCTCAAGAGTTTTGAAAAGGCCAAAGAATCTTGGGAGATGATTTCAGAAGAGAAGCTGGAAC
AGAACACCATAGTGAAAGAGCAGGGCAGAGTGTACTTCAAGGAAGGCAGATACAAGCAAGCTTTACTACAGTGTAAGAAG
ATTGTGTCCTGGCTGGAATATGAGTCTAGTTTTTCCAATGAGGAAGCACAGAAGGCACAGGCCCTTCGACTGGCGTCTCA
CCTCGACCTGGCCATGTGTCAGCTGAAACTACAGGCCTTCTCTGCTGCCATTGAAAGCTGTAACAAGGCCCTAGAACTGG
ACAGTAACAACGAGAAGGGCCCCTTCCGCCGGGGAGAGGCCCACCTGGTGGTGAATTACTTTGAACTGGCTCGGGCTGAC
TTCCAGAAGGTCCTGGAGCTCTACCCCAACAACAAAGCCGCCAGGGCCCAGCTGGCTGTGTGTCAGCAGCGGATCCGCAG
GCAGCTTGCCCGGAAGAAGTTCTATGCCAAAATGTTTGAGAGGCTGGCTGAGGAGGAGAACAAGGCCAACGCAGAGCCTT
GCTCAGGAGACCATCCCACTGACACAGAGATGAAGGCGGAGTGGAAGAGCAACACGGCAGGGAGCCAGTCTCAGGTGGAG
ACAGAAGCA

Alignment

ORF - retro_pabe_3518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTAEEMKATESGAQSAPLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSS
          MTA.EMKATES.AQ..PLP...V..SPKQDEGVLKVIKREGTGTEMPM.GD.VFVHYTGWLL.GTKFDSS
Retrocopy MTAKEMKATESAAQPEPLPKKEVEVSPKQDEGVLKVIKREGTGTEMPMTGDLVFVHYTGWLLEGTKFDSS

Parental  LDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPP-NATLVFEVELFEFKG
          ...KD..SFDLGKGEVIKAWDIA.A.MKVGEVCHITCKPEYA.GS.GSPP..PP.NATLVFEVELF..K.
Retrocopy VGGKDRLSFDLGKGEVIKAWDIAVAIMKVGEVCHITCKPEYA*GSVGSPPTVPP>NATLVFEVELF--KE

Parental  EDLTEEEDGGIIRRIQTRGEGYAKPNEGAIVEVALEGYYKDQLFDQRELRFEIGEGENLDLPYGLERAIQ
          EDLTEEEDGGI.RRI.TRGEGY.KP.EG...EVAL.G..KDQLFDQR.LRFE...GENLDLPY.LERAIQ
Retrocopy EDLTEEEDGGIVRRIGTRGEGYVKPDEGTMLEVALKGCCKDQLFDQRALRFEVSVGENLDLPYDLERAIQ

Parental  RMEKGEHSIVYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEMNSEEKLEQSTIVKERGTV
          ..EKGEHS.VYL.PSYAFGSVGKEKFQIP.NAELKYELHLKSFEKAKESWEM.SEEKLEQ.TIVKE.G.V
Retrocopy HLEKGEHSTVYLRPSYAFGSVGKEKFQIPSNAELKYELHLKSFEKAKESWEMISEEKLEQNTIVKEQGRV

Parental  YFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD
          YFKEG.YKQALLQ.KKIVSWLEYESSFSNEEAQKAQALRLASHL.LAMC.LKLQAFSAAIESCNKALELD
Retrocopy YFKEGRYKQALLQCKKIVSWLEYESSFSNEEAQKAQALRLASHLDLAMCQLKLQAFSAAIESCNKALELD

Parental  SNNEKGLFRRGEAHLAVNDFELARADFQKVLQLYPSNKAAKTQLAVCQQRIRRQLAREKKLYANMFERLA
          SNNEKG.FRRGEAHL.VN.FELARADFQKVL.LYP.NKAA..QLAVCQQRIRRQLAR.KK.YA.MFERLA
Retrocopy SNNEKGPFRRGEAHLVVNYFELARADFQKVLELYPNNKAARAQLAVCQQRIRRQLAR-KKFYAKMFERLA

Parental  EEENKAKAEASSGDHPADAEMKEEQKSSTAGSQPQVETEA
          EEENKA.AE..SGDHP.D.EMK.E.KS.TAGSQ.QVETEA
Retrocopy EEENKANAEPCSGDHPTDTEMKAEWKSNTAGSQSQVETEA

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	187.60 RPM
SRP007412_cerebellum	0.00 RPM	173.65 RPM
SRP007412_heart	0.00 RPM	50.39 RPM
SRP007412_kidney	0.00 RPM	135.54 RPM
SRP007412_liver	0.00 RPM	85.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3518 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3518 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007605	1 retrocopy	retro_btau_561,
Callithrix jacchus	ENSCJAG00000018746	1 retrocopy	retro_cjac_436,
Dasypus novemcinctus	ENSDNOG00000011244	1 retrocopy	retro_dnov_894,
Homo sapiens	ENSG00000004478	5 retrocopies	retro_hsap_3085, retro_hsap_4162, retro_hsap_4165, retro_hsap_4264, retro_hsap_4266,
Gorilla gorilla	ENSGGOG00000010471	4 retrocopies	retro_ggor_2120, retro_ggor_2852, retro_ggor_2854, retro_ggor_2855,
Macaca mulatta	ENSMMUG00000007405	1 retrocopy	retro_mmul_1969,
Nomascus leucogenys	ENSNLEG00000002835	1 retrocopy	retro_nleu_2291,
Pongo abelii	ENSPPYG00000004149	4 retrocopies	retro_pabe_2607, retro_pabe_2611, retro_pabe_3383, retro_pabe_3518 ,
Pongo abelii	ENSPPYG00000010852	5 retrocopies	retro_pabe_1654, retro_pabe_1686, retro_pabe_2364, retro_pabe_2365, retro_pabe_998,
Pongo abelii	ENSPPYG00000012604	1 retrocopy	retro_pabe_1105,
Pan troglodytes	ENSPTRG00000004529	3 retrocopies	retro_ptro_2083, retro_ptro_3000, retro_ptro_3001,