RetrogeneDB ID: retro_ptro_2054

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:60868522..60869170(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSPTRG00000012504
• Aliases: None
• Description: None

Sequence

>retro_ptro_2054
ATGTCTCAGGAACCTGCCCCACCTCTACCTAGAGATAAGTCTTTTTGTCCCATAGTAGAAAGCTAGTGTTATACAAAGAT
CAAAATAGTAAAATGTTGAACACATAGACAATTAATAACTTCAGTTTTTGTCAAGAGGAAATGGGTGAGGTGTTAAAAAG
TTCCAAATTTTCACCTGGCCCAAATGACAAAATGAAATGGTGCCTGAGGGTAAACCCAAAAGCATTAGATAATGAAAGTA
AAGACTACTTGGTCCTTATATTTGCTTTTAGTCAGATGCCCCAAAAGTGAAGTGTGAGCAAAATTCAAATGTTCCCTTCT
GAATGCTAAAAGGGAAGAAACAAAAGCAATGGAAAGCCAAAGAGCATATCAATTTGTGCAAGGGAAGGGCTGGGATTTTT
AAAAATTCATTAGAAGAGACCTTTTGCTTGACAAAGCTAATAGTCTTTGACCAGATGACAAGCTTACATTATTTTACGAG
ATGAGTGTGATCCAAGATTCAGTAAACAAATCAGGACATACTAATACAAATACTTTGAAGATGCCTGAGGGTCGACTAGG
AGAAGACTGAGGTAATCTCTGGGAAAACACAAGATTTATAGACTGCAGTTTTTTAGTGAGAGGACAAGAATTTAAAGCTC
ATAAATCT

Alignment

ORF - retro_ptro_2054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.36 %
• Parental protein coverage: 55.1 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSREPTPPLPGDMSTGPIAESWCYTQVKVV-KFSYMWTINNFSFCREEMGEVLKSSTFSSGPSDKMKWCL
          MS.EP.PPLP.D.S..PI.ES.CYT..K.V.K.....TINNFSFC.EEMGEVLKSS.FS.GP.DKMKWCL
Retrocopy MSQEPAPPLPRDKSFCPIVES*CYTKIKIV<KMLNT*TINNFSFCQEEMGEVLKSSKFSPGPNDKMKWCL

Parental  RVNPKGLDDESKDYL-SLYLLLVSCPKSEVRAKFKFSLLNAKREETKAMESQRAYRFVQGKDWGFKKFIR
          RVNPK.LD.ESKDYL.SLYLLLV.CPKSEV.AKFK.SLLNAKREETKAMESQRAY.FVQGK.W.F.KFIR
Retrocopy RVNPKALDNESKDYL>SLYLLLVRCPKSEV*AKFKCSLLNAKREETKAMESQRAYQFVQGKGWDF*KFIR

Parental  RDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDCSFFVRG
          RD.LLD.AN.L.PDDKLTLF.E.SV.QDSVN.SGHTNTNTLK.PE.RL.ED.GNLWENTRF.DCSF.VRG
Retrocopy RDLLLDKANSL*PDDKLTLFYEMSVIQDSVNKSGHTNTNTLKMPEGRLGED*GNLWENTRFIDCSFLVRG

Parental  QEFKAHKS
          QEFKAHKS
Retrocopy QEFKAHKS

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	11.51 RPM
SRP007412_cerebellum	0.00 RPM	14.02 RPM
SRP007412_heart	0.00 RPM	16.03 RPM
SRP007412_kidney	0.03 RPM	23.51 RPM
SRP007412_liver	0.00 RPM	9.56 RPM
SRP007412_testis	0.00 RPM	9.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2054 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2054 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2054 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054 ,