RetrogeneDB ID: retro_ptro_829

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:68785127..68785775(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC20
• Ensembl ID: ENSPTRG00000005695
• Aliases: None
• Description: zinc finger, DHHC-type containing 20 [Source:HGNC Symbol;Acc:20749]

Sequence

>retro_ptro_829
ATGGCGCCCTGGACGCTGTCTCGCTGCTGCCACTGCGTCATGGGCTGGGTGCCTGTGCTCCTCATCACCTTCGTGGTCAT
CTGGTCCTACTACGCGTACGTGGTGGAGCTGTGCGTGTTTACTATTTTTGGAAATGAAGAAAATGGAAAGACCGTGTTTT
ACCTTGTGGCTTTCCCTCTGTTTTTTTTATGTTTGTATGGTCCTATTGGATGACAATTTTCACATCTCCTGCTTCCCCTT
CCAAAGAATTCTACTTGTCCAATTCTGAAAAGGAACGTTATGGAAAAGAATTCAGCCAAGAAAGACAACAAGAAATTTTG
AGAAGAGCAGCAAGAGCTTTACCTATCTGTACCACGTCAGTTTCAAAAACTGTCAGATATTGTGAAAAATGTCAGCTGAT
TAAACCTGATCGGGCGCATCACTGCTCAACATGTGACTCATGTATTCTTAAGATGGATCATCACTGTCCTTGGGTGAATA
ACTGTGTGGGATTTTCTAATTACAAATTCTTCCTGCTGTTTTTATTGTATTCCCTATTATATTGCCTTTTCGTGGCTGCC
AACAGTTTTAGAGTACTTTATAAAATTTTGGACGAATGAACTGACAGATACGCGTGCAAAATTCCACGTACTTTTTCTTT
TCTGTGTC

Alignment

ORF - retro_ptro_829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 59.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPWTLWRCCQRVVGWVPVLFITFVVVWSYYAYVVELCVFTIFGNEENGKTVVYLVAFHLFFV-MFVWSY
          MAPWTL.RCC..V.GWVPVL.ITFVV.WSYYAYVVELCVFTIFGNEENGKTV.YLVAF.L....MFVWSY
Retrocopy MAPWTLSRCCHCVMGWVPVLLITFVVIWSYYAYVVELCVFTIFGNEENGKTVFYLVAFPLXXX<MFVWSY

Parental  WMTIFTSPASPSKEFYLSNSEKERYEKEFSQERQQEILRRAARALPIYTTSASKTIRYCEKCQLIKPDRA
          WMTIFTSPASPSKEFYLSNSEKERY.KEFSQERQQEILRRAARALPI.TTS.SKT.RYCEKCQLIKPDRA
Retrocopy WMTIFTSPASPSKEFYLSNSEKERYGKEFSQERQQEILRRAARALPICTTSVSKTVRYCEKCQLIKPDRA

Parental  HHCSACDSCILKMDHHCPWVNNCVGFSNYKFFLLFLLYSLLYCLFVAA-TVLEYFIKFWTNELTDTRAKF
          HHCS.CDSCILKMDHHCPWVNNCVGFSNYKFFLLFLLYSLLYCLFVAA.TVLEYFIKFWTNELTDTRAKF
Retrocopy HHCSTCDSCILKMDHHCPWVNNCVGFSNYKFFLLFLLYSLLYCLFVAA>TVLEYFIKFWTNELTDTRAKF

Parental  HVLFLFFV
          HVLFLF.V
Retrocopy HVLFLFCV

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	0.02 RPM	7.90 RPM
SRP007412_cerebellum	0.11 RPM	12.15 RPM
SRP007412_heart	0.03 RPM	3.70 RPM
SRP007412_kidney	0.03 RPM	4.13 RPM
SRP007412_liver	0.00 RPM	2.85 RPM
SRP007412_testis	0.11 RPM	67.45 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_829 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_829 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1211
Gorilla gorilla	retro_ggor_943
Macaca mulatta	retro_mmul_1288

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012155	2 retrocopies	retro_chof_1627, retro_chof_2008,
Cavia porcellus	ENSCPOG00000011489	1 retrocopy	retro_cpor_303,
Equus caballus	ENSECAG00000016465	1 retrocopy	retro_ecab_683,
Homo sapiens	ENSG00000180776	1 retrocopy	retro_hsap_1211,
Gorilla gorilla	ENSGGOG00000000435	2 retrocopies	retro_ggor_1003, retro_ggor_943,
Macaca mulatta	ENSMMUG00000007373	1 retrocopy	retro_mmul_1288,
Pongo abelii	ENSPPYG00000005201	1 retrocopy	retro_pabe_1081,
Pan troglodytes	ENSPTRG00000005695	1 retrocopy	retro_ptro_829 ,
Pan troglodytes	ENSPTRG00000014829	1 retrocopy	retro_ptro_2171,
Tarsius syrichta	ENSTSYG00000003013	1 retrocopy	retro_tsyr_998,