RetrogeneDB ID: retro_ggor_2173

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:52070864..52071473(+)
• Located in intron of: ENSGGOG00000023071

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000141580
• Ensembl ID: ENSGGOG00000006132
• Aliases: None
• Description: None

Sequence

>retro_ggor_2173
AAAGGCCTCTGTGTCCTTTGTCCCAATAGTAACAACTCCCTCCTGGCCTTTCTGGGCACGCACACGGGCCATGTGCAGCT
TGTGGACCTGGCCAGCACAGAGAAGCCACCAGTGGACATTCCTGCACACGAGGGTGTCCTGAGCTGCAGTGCACTCAAAC
TGCAGGGAACAAGAATTGCAACTGCATCTGAGAAAGGGACCCTTATAAGAATATTTGATACTTCCTCAGGACATTTAATT
CAGGAACTGCGAAGAGGATCTCAAGCAGCCAGTATTTACTGCATTAACTTCAATCAGGATGCGTCCCTCATCTGCGTATC
CAGCGACCATGGCACAGTGCATATTTTTGCAGCTGAAGATCCAAAAAGGAATAAACAGTCCAGTTTGGCCTCAGCCAGTT
TCCTTCCAAAATACTTCAGTTACAAGTGGAGTTTCTCCAAGTTTCAGGTTCCCTCAGGCTCTCCGTGCGTTTGTGCCTTT
GGAACACACCCAAACGCCATCATTGCAATTTGTGCAGACTGCAGCTACTACAAATTCCTGTTCAACCCCAAGGGGGAGTG
CATCTGAGATGTCTACGCGCAGTTTCTAGAGATGACTGATGACAAGCTG

Alignment

ORF - retro_ggor_2173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.09 %
• Parental protein coverage: 73.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RDLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCIALNLQGTRIATASEKGTLIR
          ..LCVLCPNSNNSLLAF.GTHTGHVQLVDLASTEKPPVDIPAHEGVLSC.AL.LQGTRIATASEKGTLIR
Retrocopy KGLCVLCPNSNNSLLAFLGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCSALKLQGTRIATASEKGTLIR

Parental  IFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAEDPKRNKQSSLASASFLPKYFS
          IFDTSSGHLIQELRRGSQAA.IYCINFNQDASLICVSSDHGTVHIFAAEDPKRNKQSSLASASFLPKYFS
Retrocopy IFDTSSGHLIQELRRGSQAASIYCINFNQDASLICVSSDHGTVHIFAAEDPKRNKQSSLASASFLPKYFS

Parental  SKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGSYYKFLFNPKGECIRDVYAQFLEMTDDKL
          .KWSFSKFQVPSGSPC.CAFGT.PNA.IAICAD.SYYKFLFNPKGECI.DVYAQFLEMTDDKL
Retrocopy YKWSFSKFQVPSGSPCVCAFGTHPNAIIAICADCSYYKFLFNPKGECI*DVYAQFLEMTDDKL

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	1.63 RPM	12.42 RPM
SRP007412_cerebellum	2.44 RPM	13.12 RPM
SRP007412_heart	0.28 RPM	2.31 RPM
SRP007412_kidney	1.88 RPM	9.98 RPM
SRP007412_liver	0.79 RPM	5.43 RPM
SRP007412_testis	5.18 RPM	17.72 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2173 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1820
Pan troglodytes	retro_ptro_1171
Pongo abelii	retro_pabe_150

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005657	1 retrocopy	retro_cpor_322,
Homo sapiens	ENSG00000141580	2 retrocopies	retro_hsap_1820, retro_hsap_1879,
Gorilla gorilla	ENSGGOG00000000589	1 retrocopy	retro_ggor_2075,
Gorilla gorilla	ENSGGOG00000006132	2 retrocopies	retro_ggor_1376, retro_ggor_2173 ,
Macropus eugenii	ENSMEUG00000013344	1 retrocopy	retro_meug_233,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330,
Mus musculus	ENSMUSG00000025173	1 retrocopy	retro_mmus_1487,
Nomascus leucogenys	ENSNLEG00000010516	1 retrocopy	retro_nleu_1227,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559,
Pan troglodytes	ENSPTRG00000009807	3 retrocopies	retro_ptro_1171, retro_ptro_1262, retro_ptro_2912,
Pteropus vampyrus	ENSPVAG00000006212	1 retrocopy	retro_pvam_158,