RetrogeneDB ID: retro_ptro_1960

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:193061571..193062039(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENOPH1
• Ensembl ID: ENSPTRG00000016218
• Aliases: None
• Description: None

Sequence

>retro_ptro_1960
GGGAATGGAGTGGATGATCTGCAACAGATGATCCAGGCCGTGGTAGATAAGGTGTGCTGGCAGATGTCCCTGGACGGAAA
GACCACCATGTTCAAACAGCTGCAGGACCACACCTGAAGGGCAGCATTCACAGCTCGGCCCATGAAAGCAGAGTTCTTTG
CAGATGTGTTTCCAGCAGTCAGGAAGTGGAAAGAGGCTGGAATGAAGGTGTATATCTATTCCTCTGGGAGTGCAGAGGCA
CAGAAACTGATATTCGGGCAGTCTGCGAAGGGAAAGATTCTTGAGCTTGTTGATGGTCCCTTTGATACCAAGATTGGACA
CAAAGTAGAGAATGAAAGTTATCAAAGGATTGCAGACTGCACTGGGGGCTCAACCAACAACATTTTGTTTCTGACAGATG
TTACTCAAGAGGCCGGTGCTGCTGAGGAAGCAGATGTGCATGTAGCGGTGGTGGTGAGACTTGGAGAC

Alignment

ORF - retro_ptro_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.05 %
• Parental protein coverage: 59.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNGVDDLQQMIQAVVDNVCWQMSLDRKTTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKV
          GNGVDDLQQMIQAVVD.VCWQMSLD.KTT..KQLQ.H..RAAFTA..MKAEFFADV.PAVRKW.EAGMKV
Retrocopy GNGVDDLQQMIQAVVDKVCWQMSLDGKTTMFKQLQDHT*RAAFTARPMKAEFFADVFPAVRKWKEAGMKV

Parental  YIYSSGSVEAQKLLFGHSTEGDILELVDGHFDTKIGHKVESESYRKIADSIGCSTNNILFLTDVTREASA
          YIYSSGS.EAQKL.FG.S..G.ILELVDG.FDTKIGHKVE.ESY..IAD..G.STNNILFLTDVT.EA.A
Retrocopy YIYSSGSAEAQKLIFGQSAKGKILELVDGPFDTKIGHKVENESYQRIADCTGGSTNNILFLTDVTQEAGA

Parental  AEEADVHVAVVVRPGN
          AEEADVHVAVVVR.G.
Retrocopy AEEADVHVAVVVRLGD

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	46.96 RPM
SRP007412_cerebellum	0.00 RPM	46.03 RPM
SRP007412_heart	0.00 RPM	12.45 RPM
SRP007412_kidney	0.03 RPM	20.74 RPM
SRP007412_liver	0.00 RPM	11.56 RPM
SRP007412_testis	0.00 RPM	14.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1960 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1960 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2900
Gorilla gorilla	retro_ggor_2010
Pongo abelii	retro_pabe_2399

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005140	2 retrocopies	retro_amel_1186, retro_amel_930,
Choloepus hoffmanni	ENSCHOG00000003283	4 retrocopies	retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Callithrix jacchus	ENSCJAG00000015251	2 retrocopies	retro_cjac_1376, retro_cjac_2375,
Equus caballus	ENSECAG00000019612	1 retrocopy	retro_ecab_164,
Erinaceus europaeus	ENSEEUG00000004274	1 retrocopy	retro_eeur_563,
Homo sapiens	ENSG00000145293	1 retrocopy	retro_hsap_2900,
Gorilla gorilla	ENSGGOG00000003719	1 retrocopy	retro_ggor_2010,
Loxodonta africana	ENSLAFG00000008619	1 retrocopy	retro_lafr_1158,
Macropus eugenii	ENSMEUG00000011458	1 retrocopy	retro_meug_1125,
Myotis lucifugus	ENSMLUG00000014460	1 retrocopy	retro_mluc_2504,
Otolemur garnettii	ENSOGAG00000002502	1 retrocopy	retro_ogar_1549,
Pongo abelii	ENSPPYG00000014887	1 retrocopy	retro_pabe_2399,
Pan troglodytes	ENSPTRG00000016218	1 retrocopy	retro_ptro_1960 ,
Tursiops truncatus	ENSTTRG00000001800	1 retrocopy	retro_ttru_1231,