RetrogeneDB ID: retro_ptro_3000

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL391076.1:99489..100396(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP4
• Ensembl ID: ENSPTRG00000004529
• Aliases: None
• Description: FK506 binding protein 4, 59kDa [Source:HGNC Symbol;Acc:3720]

Sequence

>retro_ptro_3000
ATGACAGCCAAGGAGATGAAGGCGACCGAGAGTGCGGCGCAGCCGGCGCCGCTGCCCAAGAAGGAAGTGGATGTCAGCCC
CAAACAGGATGAAGGAGTGCTGAAGGTCATCAAGAGAGAGGGCACAGGTACAGAGATGCCCATGACTGGGGACCTAGTCT
TTGTCCACTACACTGGCTGGCTGTTAGAGGGCACAAAGTTTGACTCCAGTGTGGATCCCAAGGACAAATTCTCCTTTGAC
CTGGGAAAAGGGGAGGTCATCAAGGCTTGGGACATTACCGTAGCAACCATGAAGGTGGGGGAGGTGGGCCACATCACCTG
CAAACCAGAATATGCCTAGAGTTCAGCAGACAGTCCTCCAACGATCCCCCCATAACGCCACGCTTGTGTTTGAGGTGGAA
TTGTTTAAGGAAGAAGATCTGACGGAAGAGGAAGATGGGGGAATCATCCGCAGAATAGGGACTCGTGGTGAAGGCTATGT
CAAGCCCGATGAGGGCGCTATGGTGGAGGTTGCGCTGGAAGGGTGCTGCAAGGACCAGCTCTTTGACCAACGAGCGCTCC
GCTTTGAGGTTAGCGAGGGGGAGAACCTGGATCTGCCTTATGATCTCGAGAGGGCCATTCAGCACTTGGAGAAAGGAGAA
CATTCCATTGTGTACCTCAAGCCCAGCTATGCTTTTGGCAGTGTTGGGAAGGAAAAGTTCCAAATCCCACCAAATGCCGA
GCTGAAATATGAATTACATCTCAAGAGTTTTGAAAAGGCCAAGGAATCTTGGGAGATGATTTCAGAAGAGAAGCTGGAAC
AGAACACCATAGTGAAAGAGCAGGGCAGTGTGTACTTCAAGGAAGGCAAATACAAGCAAGCTTTACTACAGTGTAAGAAG
ATTGTGTCCTGGCTGGAATATGAGTCT

Alignment

ORF - retro_ptro_3000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTAEQTKATESGAQSAPLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSS
          MTA...KATES.AQ.APLP...VD.SPKQDEGVLKVIKREGTGTEMPM.GD.VFVHYTGWLL.GTKFDSS
Retrocopy MTAKEMKATESAAQPAPLPKKEVDVSPKQDEGVLKVIKREGTGTEMPMTGDLVFVHYTGWLLEGTKFDSS

Parental  LDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPP-NATLVFEVELFEFKG
          .D.KDKFSFDLGKGEVIKAWDI..ATMKVGEV.HITCKPEYA..SA.SPP.IPP.NATLVFEVELF..K.
Retrocopy VDPKDKFSFDLGKGEVIKAWDITVATMKVGEVGHITCKPEYA*SSADSPPTIPP>NATLVFEVELF--KE

Parental  EDLTEEEDGGIIRRIQTRGEGYAKPNEGAIVEVALEGYYKDQLFDQRELRFEIGEGENLDLPYGLERAIQ
          EDLTEEEDGGIIRRI.TRGEGY.KP.EGA.VEVALEG..KDQLFDQR.LRFE..EGENLDLPY.LERAIQ
Retrocopy EDLTEEEDGGIIRRIGTRGEGYVKPDEGAMVEVALEGCCKDQLFDQRALRFEVSEGENLDLPYDLERAIQ

Parental  RMEKGEHSIVYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEMNSEEKLEQSTIVKERGTV
          ..EKGEHSIVYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEM.SEEKLEQ.TIVKE.G.V
Retrocopy HLEKGEHSIVYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEMISEEKLEQNTIVKEQGSV

Parental  YFKEGKYKQALLQYKKIVSWLEYES
          YFKEGKYKQALLQ.KKIVSWLEYES
Retrocopy YFKEGKYKQALLQCKKIVSWLEYES

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	180.92 RPM
SRP007412_cerebellum	0.00 RPM	296.68 RPM
SRP007412_heart	0.00 RPM	75.66 RPM
SRP007412_kidney	0.03 RPM	124.33 RPM
SRP007412_liver	0.00 RPM	122.72 RPM
SRP007412_testis	0.00 RPM	391.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3000 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3000 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 24 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,
Pan troglodytes	ENSPTRG00000004529	3 retrocopies	retro_ptro_2083, retro_ptro_3000 , retro_ptro_3001,
Pan troglodytes	ENSPTRG00000011708	1 retrocopy	retro_ptro_906,
Pan troglodytes	ENSPTRG00000013163	2 retrocopies	retro_ptro_2983, retro_ptro_818,