RetrogeneDB ID: retro_ptro_3205

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:45837771..45838315(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLLP
• Ensembl ID: ENSPTRG00000008151
• Aliases: None
• Description: plasmolipin [Source:HGNC Symbol;Acc:18553]

Sequence

>retro_ptro_3205
ATGGCCGAGTTCCCGTCAAAAGTGAGCACGCGGACCAGCAGTCCCGCGCAGGACGCTGGAGCCTTGGTGTAGGCGCTGCG
CACGGACCTGGGCTTCGTGCGCTCCCGCCTCGGGCGTTCATGCTGCTGCAGCTGGTGCTGGAGCTGCTGGTGTGGGCCCT
GATTGCGGACACCCCGTACCACCTGTACCCGGCCTATGGCTGGGTGATGTTCGTATCTGTCTTCCTCTGGCTGGTGACAA
TCGTCTTCTTCACCCTCTACCTGTTTCAGCTGCACATGAAGTTGTACATGGTGCCCTGGCCACTAGTGCTAATGATGTTT
AACGTCAGTGCCACCCTTCTTTACGTCACCGCCTTCATCGCCTGCTCTGCGGCAGTTGACCTGACGTCCCTGAAGGGCAC
GCAGCCGTATAACCAGCGTGCGGCTACCTCGTTCTTTGCGTGTTTGGTGATGATCGCCTACGGAGTGAGCGCCTTCTTCA
GCTACCATGCCTGGCGAGGAGTAGGCAGCAATGCGCCACCAGTCAGATGGCTGGCGGCTATGCC

Alignment

ORF - retro_ptro_3205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEFPSKVSTRTSSPAQGAEASVSALRPDLGFVRSRLG-ALMLLQLVLGLLVWALIADTPYHLYPAYGWV
          MAEFPSKVSTRTSSPAQ.A.A.V.ALR.DLGFVRSRLG.A.MLLQLVL.LLVWALIADTPYHLYPAYGWV
Retrocopy MAEFPSKVSTRTSSPAQDAGALV*ALRTDLGFVRSRLG<AFMLLQLVLELLVWALIADTPYHLYPAYGWV

Parental  MFVAVFLWLVTIVLFILYLFQLHMKLYMVPWPLVLMIFNISATVLYITAFIACSAAVDLTSLRGTRPYNQ
          MFV.VFLWLVTIV.F.LYLFQLHMKLYMVPWPLVLM.FN.SAT.LY.TAFIACSAAVDLTSL.GT.PYNQ
Retrocopy MFVSVFLWLVTIVFFTLYLFQLHMKLYMVPWPLVLMMFNVSATLLYVTAFIACSAAVDLTSLKGTQPYNQ

Parental  RAAASFFACLVMIAYGVSAFFSYQAWRGVGSNA-ATSQMAGGYA
          RAA.SFFACLVMIAYGVSAFFSY.AWRGVGSNA.ATSQMAGGYA
Retrocopy RAATSFFACLVMIAYGVSAFFSYHAWRGVGSNA<ATSQMAGGYA

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	82.01 RPM
SRP007412_cerebellum	0.00 RPM	21.01 RPM
SRP007412_heart	0.00 RPM	0.85 RPM
SRP007412_kidney	0.00 RPM	39.72 RPM
SRP007412_liver	0.00 RPM	3.73 RPM
SRP007412_testis	0.00 RPM	0.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3205 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3205 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3205 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4816
Pongo abelii	retro_pabe_3744
Macaca mulatta	retro_mmul_2569
Callithrix jacchus	retro_cjac_4155

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012103	1 retrocopy	retro_cjac_4155,
Homo sapiens	ENSG00000102934	1 retrocopy	retro_hsap_4816,
Loxodonta africana	ENSLAFG00000008636	1 retrocopy	retro_lafr_145,
Macaca mulatta	ENSMMUG00000008924	1 retrocopy	retro_mmul_2569,
Nomascus leucogenys	ENSNLEG00000002825	1 retrocopy	retro_nleu_2191,
Oryctolagus cuniculus	ENSOCUG00000007353	1 retrocopy	retro_ocun_685,
Pongo abelii	ENSPPYG00000007385	1 retrocopy	retro_pabe_3744,
Pan troglodytes	ENSPTRG00000008151	1 retrocopy	retro_ptro_3205 ,