RetrogeneDB ID: retro_ptro_1062

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:56316788..56317267(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBFA
• Ensembl ID: ENSPTRG00000010137
• Aliases: None
• Description: Ribosome binding factor A (Putative) [Source:UniProtKB/TrEMBL;Acc:K7AW40]

Sequence

>retro_ptro_1062
TGGTCTGAAGCTCTTTCTCTACGATCTCACTTTACTTACAAACCATCTAAGTTGGAAGTCCTGGTGAAGAATACCTCAAA
GAAAATTAAGGAGGTCCACATATGCTTAAGGACCCTGGATGGCCTTCTCTGTCAAGCATTCACAGATTGCAGTGCACCTG
CGATGTGAAGCAAGATATCTACAACCTGAATTTGTAGCTTTCCAAGGTATGTCTGACTTTAGACTTCTCAGCCTTCTATG
TATATCAGAAGACACCTCTTTTTGCTGAGCAAAATGAGCACACAGAAGCCAACTTACAGAAAAGCACTGTACAAATGAAG
CATCTTTTGATGTCTCAACAGATCTTGAGTAATGTGGTGCCAATACAGTTTGTTCAAGACAAACAAAATACAGCTCTAGC
TGAGATTGATCGGTTACTGACAATGGTTGACTGTAGACCATCACATGAATAAGACTTTATACCAAATGATTTCAGGGAA

Alignment

ORF - retro_ptro_1062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.12 %
• Parental protein coverage: 54.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WYESPSLGSHSTYKPSKLEFLMRSTSKKTRKEDHARLRALNGLLYKALTD-LLCTPEVSQELYDLNVELS
          W.E..SL.SH.TYKPSKLE.L...TSKK..KE.H..LR.L.GLL..A.TD.L.CT..V.Q..Y.LN..LS
Retrocopy WSEALSLRSHFTYKPSKLEVLVKNTSKKI-KEVHICLRTLDGLLCQAFTD<LQCTCDVKQDIYNLNL*LS

Parental  KVSLTPDFSACRAYWKTTLSAEQNAHMEAVLQRSAAHMRHLLMSQQTLRNVPPIVFVQDKGNAALAELDQ
          KV.LT.DFSA...Y.KT.L.AEQN.H.EA.LQ.S...M.HLLMSQQ.L.NV.PI.FVQDK.N.ALAE.D.
Retrocopy KVCLTLDFSAFYVYQKTPLFAEQNEHTEANLQKSTVQMKHLLMSQQILSNVVPIQFVQDKQNTALAEIDR

Parental  LLAVADFGPRDERDNFVQNDFRD
          LL...D..P..E.D.F..NDFR.
Retrocopy LLTMVDCRPSHE*D-FIPNDFRE

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	11.92 RPM
SRP007412_cerebellum	0.00 RPM	23.84 RPM
SRP007412_heart	0.00 RPM	17.69 RPM
SRP007412_kidney	0.00 RPM	25.58 RPM
SRP007412_liver	0.00 RPM	51.23 RPM
SRP007412_testis	0.00 RPM	15.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1062 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1062 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1062 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_146

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036297	1 retrocopy	retro_btau_1031,
Cavia porcellus	ENSCPOG00000000170	1 retrocopy	retro_cpor_911,
Equus caballus	ENSECAG00000008292	1 retrocopy	retro_ecab_146,
Pan troglodytes	ENSPTRG00000010137	1 retrocopy	retro_ptro_1062 ,