RetrogeneDB ID: retro_ptro_211

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:139268765..139269637(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX56
• Ensembl ID: ENSPTRG00000019147
• Aliases: None
• Description: None

Sequence

>retro_ptro_211
TTGATTCGGAGTAAGTCTCTGCTCTTTGTCAACACTCTAGAGTGGAGTTACTGGCTACACCTGTTTCTGGAGCAGTTCAG
CATCCCCACCTGTGTGCTCAGTGGAGCCCTTCCCCTGCTCTCCAGGTGCCACATCATCTCACAGTTCAACCAAGGCTTCT
AGGACTGTGTCATAGCAACTGATGCTGAATTCCTGGGGGCCCCAGTCAAGGGCAAGCATCAGGGCGAGGGGCCAAAGGGG
ACAAGGCCTCTAATATGGAGGCAGGGGTGGCCCGGGGCATAGACTTCCACTATGTGTCTGCTGTGCTCAACTTTGATCTT
CCCCCCACCCCCGAGGCCTACATCCATCAAACCGGCAGGACAGCGCGCTACAACCCAGGCATAGTCTTAACCTTTGTGTT
GCCCAGGGAACAGTCCCACTTGGGCAAGATTGAGGACCTTCTCAGTGAAGAGAACAAGGGCCCCATCCTGCTCCCCTACC
AGTTCCGGATGGAGAAGATTGAGGGCTTCCGCTATCGCTGCTGGGATGCCATGCACTCAGTGGCTAAACAGGCCATTCGA
GAGGTGAGATTGAAGGAGACCAAGGAGGAGCTTCTGCACTCTAAGAAGCTCAAGATGTACTTTGAAGACAACCCTAGGGA
CCTCCAGGTGCTGCAGCATGACCTGCCATTGCACCCCGCGGTGGTGAAGCCCCACCTGGGCCATGTTCCTGACTACCTGG
TTCCTACTGCTCTCCATGGCCTGGTGCACCCTCACAAGAAGCGGAAGAGGCTGTCTTCCTCTCATAGGAAGGCCAAGAGA
GCAAAGTCCCAGAACCCACTGCACAGTTTCAAGCACAAAGGAAAGAAATTCAGACCTGCAGCAAAGTCCTCC

Alignment

ORF - retro_ptro_211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.32 %
• Parental protein coverage: 53.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIRGKSLLFVNTLERSYRLRLFLEQFSIPTCVLNGELPLRSRCHIISQFNQGFYDCVIATDAEVLGAPVK
          LIR.KSLLFVNTLE.SY.L.LFLEQFSIPTCVL.G.LPL.SRCHIISQFNQGF.DCVIATDAE.LGAPVK
Retrocopy LIRSKSLLFVNTLEWSYWLHLFLEQFSIPTCVLSGALPLLSRCHIISQFNQGF*DCVIATDAEFLGAPVK

Parental  GKRRGRGPKG-DKASDLEAGVARGIDFHHVSAVLNFDLPPTPEAYIHRAGRTARANNPGIVLTFVLPTEQ
          GK..G.GPKG.DKAS..EAGVARGIDFH.VSAVLNFDLPPTPEAYIH..GRTAR.N.PGIVLTFVLP.EQ
Retrocopy GKHQGEGPKG<DKASNMEAGVARGIDFHYVSAVLNFDLPPTPEAYIHQTGRTARYN-PGIVLTFVLPREQ

Parental  FHLGKIEELLSGENRGPILLPYQFRMEEIEGFRYRCRDAMRSVTKQAIREARLKEIKEELLHSEKLKTYF
          .HLGKIE.LLS.EN.GPILLPYQFRME.IEGFRYRC.DAM.SV.KQAIRE.RLKE.KEELLHS.KLK.YF
Retrocopy SHLGKIEDLLSEENKGPILLPYQFRMEKIEGFRYRCWDAMHSVAKQAIREVRLKETKEELLHSKKLKMYF

Parental  EDNPRDLQLLRHDLPLHPAVVKPHLGHVPDYLVPPALRGLVRPHKKRKKLSSSCRKAKRAKSQNPLRSFK
          EDNPRDLQ.L.HDLPLHPAVVKPHLGHVPDYLVP.AL.GLV.PHKKRK.LSSS.RKAKRAKSQNPL.SFK
Retrocopy EDNPRDLQVLQHDLPLHPAVVKPHLGHVPDYLVPTALHGLVHPHKKRKRLSSSHRKAKRAKSQNPLHSFK

Parental  HKGKKFRPTAKPS
          HKGKKFRP.AK.S
Retrocopy HKGKKFRPAAKSS

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	44.61 RPM
SRP007412_cerebellum	0.00 RPM	58.54 RPM
SRP007412_heart	0.00 RPM	15.30 RPM
SRP007412_kidney	0.00 RPM	55.36 RPM
SRP007412_liver	0.00 RPM	43.24 RPM
SRP007412_testis	0.00 RPM	23.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_211 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_211 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000012031	1 retrocopy	retro_ggor_2092,
Pan troglodytes	ENSPTRG00000019147	1 retrocopy	retro_ptro_211 ,