RetrogeneDB ID: retro_ptro_1106

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:49026248..49026800(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPRD1A
• Ensembl ID: ENSPTRG00000009974
• Aliases: None
• Description: regulation of nuclear pre-mRNA domain-containing protein 1A [Source:RefSeq peptide;Acc:NP_001229515]

Sequence

>retro_ptro_1106
GCTCTGTGTGGTGATAAGAAGCCTAGGAAGCAAATTTATAAACAGATAAAGATGAATGAAAATAAAAACTGTTCCTCTCT
GGGATCTGCAAGTGAGCCACCACCACAGACTCTAAATCTCGTGACAGCATTACAAAATCTAGAAAATGCAGCCTTGGGTG
ATGCAGGAGTTCACTAGAGGATCACTTTTTTGCCTGCTGTAGACCAAGAAGTATCTCTACTAGATAAAATAGCAGATAAA
GAACCTGGAGAAAGGCTTTCTAAAATGATGGATGCATGTATGTTGCCGGCAGATTACAATGGCAGAATGGCAGCAGAAAT
AGATGAGAGGAAGCAACTCACTCGAATGTTAGCAGATTTTCTTCATTGTCCAATGGAAGCCCTTGCAGAGAAAGCATAAA
TTGGAAGAATACAAGTGCAAGTGAGCCAGAGTTTCCCTGGTGTGCAAAGAATTCAGGTCCCCGATCCAGAGCCTGTCAGA
CTAATCTTGACTACCCAATGTCACTGGCAGCTGCATGCACCTGCCCTTTGCAGGGACATCTACAGTGAAGAT

Alignment

ORF - retro_ptro_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 59.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALYGDKKPRKRTYEQIKVDENENCSSLGSPSEPP-QTLDLVRALQDLENAASGDAAVHQRIASLPVEVQE
          AL.GDKKPRK..Y.QIK..EN.NCSSLGS.SEPP.QTL.LV.ALQ.LENAA.GDA.VH.RI..LP...QE
Retrocopy ALCGDKKPRKQIYKQIKMNENKNCSSLGSASEPPPQTLNLVTALQNLENAALGDAGVH*RITFLPAVDQE

Parental  VSLLDKITDKESGERLSKMVEDACMLLADYNGRLAAEIDDRKQLTRMLAD-FLRCQKEALAEKEHKLEEY
          VSLLDKI.DKE.GERLSKM..DACML.ADYNGR.AAEID.RKQLTRMLAD.F...Q...L....HKLEEY
Retrocopy VSLLDKIADKEPGERLSKMM-DACMLPADYNGRMAAEIDERKQLTRMLAD>FFIVQWKPL-QRKHKLEEY

Parental  KRKLARVSLVRKELRSRIQSLPDLSRLPNVTGSHMHLPFAG-DIYSED
          K.K.ARVSLV.KE.RS.IQSL.D.S.LPNVTGS.MHLPFAG.DIYSED
Retrocopy KCK*ARVSLVCKEFRSPIQSLSD*S*LPNVTGSCMHLPFAG<DIYSED

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	41.29 RPM
SRP007412_cerebellum	0.07 RPM	52.55 RPM
SRP007412_heart	0.00 RPM	19.73 RPM
SRP007412_kidney	0.00 RPM	22.41 RPM
SRP007412_liver	0.00 RPM	10.61 RPM
SRP007412_testis	0.00 RPM	38.15 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1106 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1106 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1237
Pongo abelii	retro_pabe_1352
Macaca mulatta	retro_mmul_1562

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007025	1 retrocopy	retro_eeur_245,
Gorilla gorilla	ENSGGOG00000007369	1 retrocopy	retro_ggor_1237,
Macaca mulatta	ENSMMUG00000018777	1 retrocopy	retro_mmul_1562,
Monodelphis domestica	ENSMODG00000000399	1 retrocopy	retro_mdom_360,
Nomascus leucogenys	ENSNLEG00000006228	1 retrocopy	retro_nleu_1323,
Pongo abelii	ENSPPYG00000009111	1 retrocopy	retro_pabe_1352,
Pan troglodytes	ENSPTRG00000009974	1 retrocopy	retro_ptro_1106 ,
Vicugna pacos	ENSVPAG00000001641	1 retrocopy	retro_vpac_62,