RetrogeneDB ID: retro_ptro_9

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:19345221..19345941(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042509
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000013661
• Aliases: None
• Description: None

Sequence

>retro_ptro_9
ATGCTGCTGCAGCCCGCGCCGTGCGCCCCGAGCGCGGGCTTCCCGCGGCCCCTGGCCGCCCCCGGCGCCATGCACGGCTC
GCAGAAGGACACCACGTTCACCAAGATCTTCGTGGGCGGCCTGCCGTACCACACTACCGACGCCTCGCTCAGGAAGTACT
TCGAGGGCTTCGGCGACATCGAGGAGGCCGTGGTCATCACCGACCGCCAGACGGGCAAGTCCCGCGGCTACGGCTTCGTG
ACCATGGCCGACCGGGCGGCAGCTGAGAGGGCTTGCAAAGACCCGAACCCCATCATCGACGGCCGCAAGGCCAACGTGAA
CCTGGCATATCTGGGCGCCAAGCCGCGGAGCCTCCAGACGGGCTTTGCCATTGGGGTGCAGCAGCTGCACCCCACCTTGA
TCCAGCGGACTTACGGGCTGACCCCGCACTACATCTACCCACCAGCCATCGTGCAGCCCAGCGTGGTGATCCCAGCCGCC
CCTGTCCCGTCGCTGTCCTCGCCCTACATTGAGTACACGCCGGCCAGCCCGGCCTACGCCCAGTACCCACCGGCCACCTA
TGACCAGTACCCATACGCCGCCTCGCCTGCCACGGCTGCCAGCTTCGTGGGCTACAGCTACCCGGCCGCCGTGCCCCAGG
CCCTCTCAGCCGCAGCCCCCGCGGGCACCACCTTCGTGCAGTACCAGGCGCCGCAGCTGCAGCCTGACAGGATGCAGTGA

Alignment

ORF - retro_ptro_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLRPAPCAPSAAFPRPLAPPGAMHGSQKATTFTKIFVGGLPYHTPDASLRKYFEGFGAIEEAVVITDRQ
          M.L.PAPCAPSA.FPRPLA.PGAMHGSQK.TTFTKIFVGGLPYHT.DASLRKYFEGFG.IEEAVVITDRQ
Retrocopy MLLQPAPCAPSAGFPRPLAAPGAMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ

Parental  TGKSRGYGFVTMADRAAADRACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVQQLHPTLIQRTYGL
          TGKSRGYGFVTMADRAAA.RACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVQQLHPTLIQRTYGL
Retrocopy TGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVQQLHPTLIQRTYGL

Parental  TPHYIYPPAIVQPSVVIPAAPVPSLSSPYIEYTPASPAYAQYPPATYDQYPYAASPATAASFVGYSYPAA
          TPHYIYPPAIVQPSVVIPAAPVPSLSSPYIEYTPASPAYAQYPPATYDQYPYAASPATAASFVGYSYPAA
Retrocopy TPHYIYPPAIVQPSVVIPAAPVPSLSSPYIEYTPASPAYAQYPPATYDQYPYAASPATAASFVGYSYPAA

Parental  VPQALSAAAPAGTTFVQYQAPQLQPDRMQ
          VPQALSAAAPAGTTFVQYQAPQLQPDRMQ
Retrocopy VPQALSAAAPAGTTFVQYQAPQLQPDRMQ

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	0.20 RPM	7.35 RPM
SRP007412_cerebellum	0.11 RPM	4.41 RPM
SRP007412_heart	0.20 RPM	6.44 RPM
SRP007412_kidney	0.10 RPM	5.36 RPM
SRP007412_liver	0.16 RPM	2.00 RPM
SRP007412_testis	0.00 RPM	3.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_9 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_9 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_9 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019139	1 retrocopy	retro_cjac_2079,
Macaca mulatta	ENSMMUG00000031391	1 retrocopy	retro_mmul_1546,
Pan troglodytes	ENSPTRG00000013661	1 retrocopy	retro_ptro_9 ,