RetrogeneDB ID: retro_ptro_1578

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:20460866..20461536(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRG1
• Ensembl ID: ENSPTRG00000014272
• Aliases: None
• Description: None

Sequence

>retro_ptro_1578
AACAAGGCCACAGCACACCACCTAGGGCTGCTTAAGGCTCGTCTTGCTAAGCTTCGTCGAGAACTCATTACTCCAAAGGG
TGGTGGTAGTGGAGGTCCAGAAGAAGGTTTTGATGTGGCCAAGACAGGTGATGCTTGAATTGGATTTGTTGGTTTTCCAT
TTGTGGGGAAGTCGACACTGCTTAGTAACCTGGCAGGGGTATATTCTGAGGTGGCAGCCTATGAATTCACTACTCTGAGC
ACTGTGCCTGGTGTCATCAGATACAAAGGTGCCAAAATCCAGCTCCTGGATCTCCCAGGTATTATTGAAGGTGCCAAGGA
TGGGAAAGGTAGAGGTCGTCAATCATTGCAGTGGCCCGAACCTGTAACTTGATCCTGATTGTTCTGGATGTCCTGAAACC
TTTGGGACATAAGAAGATAATTGAAAATGAGCTGGAAGTCTTTGGCATTCACTTGAACAGCAACCACCGCCCCCCAACAC
TGGCTTTAAGAAGAAGGACAAGGGAGGCATTCATCTCACAGCCACTTGCCCACAGAGTGAGCTGGATGCTGAAACTGTGA
AGAGCATTCTGGCTGAACACAAGATTCATAATGCCGATGTGACTCTACGTAGTGATGCTACAGCTGATGACCTCATTGAT
GTGGTGGAAGAAAACAGAGTTTATATCCCC

Alignment

ORF - retro_ptro_1578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.48 %
• Parental protein coverage: 60.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFVGFPSVGKSTLLSNLAGVYSE
          NKATAHHLGLLKARLAKLRRELITPKGGG.GGP.EGFDVAKTGDA.IGFVGFP.VGKSTLLSNLAGVYSE
Retrocopy NKATAHHLGLLKARLAKLRRELITPKGGGSGGPEEGFDVAKTGDA*IGFVGFPFVGKSTLLSNLAGVYSE

Parental  VAAYEFTTLTTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQ-VIAVARTCNLILIVLDVLKPLGHKK
          VAAYEFTTL.TVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQ..IAVARTCNLILIVLDVLKPLGHKK
Retrocopy VAAYEFTTLSTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQ<IIAVARTCNLILIVLDVLKPLGHKK

Parental  IIENELEGFGIRLNS--KPP-NIGFKKKDKGGINLTATCPQSELDAETVKSILAEYKIHNADVTLRSDAT
          IIENELE.FGI.LNS...PP.N.GFKKKDKGGI.LTATCPQSELDAETVKSILAE.KIHNADVTLRSDAT
Retrocopy IIENELEVFGIHLNSNHRPP<NTGFKKKDKGGIHLTATCPQSELDAETVKSILAEHKIHNADVTLRSDAT

Parental  ADDLIDVVEGNRVYIP
          ADDLIDVVE.NRVYIP
Retrocopy ADDLIDVVEENRVYIP

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	42.58 RPM
SRP007412_cerebellum	0.00 RPM	56.03 RPM
SRP007412_heart	0.00 RPM	32.47 RPM
SRP007412_kidney	0.00 RPM	40.56 RPM
SRP007412_liver	0.00 RPM	35.78 RPM
SRP007412_testis	0.74 RPM	599.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1578 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1578 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2231
Gorilla gorilla	retro_ggor_1665

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578 ,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,