RetrogeneDB ID: retro_ggor_2109

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:114861290..114862005(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM64A
• Ensembl ID: ENSGGOG00000012309
• Aliases: None
• Description: None

Sequence

>retro_ggor_2109
ATGGCTTCCTAGTGGCAGGGAATGGGGGCCTCTGTGCGCCGGAAATCTCTACAGCACCAGGAGCAGCTGGAGGACAGCAA
GGAGCTGCAGCCTTTGGCCAGCCATCAGGAGACCTCCACCGGGGCCCTGAGTACCCTAAGCAGACAGTTCCAAAGGAGGC
TGCCCCTGAGAGCTGTCAATCTCAGCCTCCAGGCAGGCCCCTCCTGGAAACGCCTGGAAACACCAGAGCCAGGGCCACAG
GGCCTCCAGGCTGCAGCTCCCTCAGCTAAGAGTGCCTTGGGTGCCAAGTCCCAGAGAATCCAGGAGTCCTGCCAAAGCAG
CACCGAATGGCTGGTGGAGACCCAGGTGAAGGCCAGGAGGAGGAAGAGAGGGGCACAGAGGGCAGTGGATCACCAACTCA
CAGCCGGAGCCACGAGAGCACCCGGCTGTCTGGAGCCGCCCCTGCCCACTCAGCCGCAGACCCCTGGGAGAAGGAGCATC
ACCACCTCTCTGCCCCATAGGCTCACGTGCCCACCCAGTAAGGCTGTCGAGGCGGGAGGCTGCCTTCCGGAGCCCCTACT
CCTCAGAAGAGCCCCTCTGCTCTCCCAGTGAGTCTGACAGTGATCGAGGGACGGCGGGGGCGGGAACTCAGCATCTCCAG
AAGCTCTCCCAAGAGCTGGACGAAGCTATTATGGCGGAAGAGAGTGGTGACATGACCGTCTCTCTCATCCATGAC

Alignment

ORF - retro_ggor_2109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASRWQSMGTSVRRRSLQHQEQLEDSKELQPVVSHQETSVGALGSLCRQFQRRLPLRAVNLNLRAGPSWK
          MAS.WQ.MG.SVRR.SLQHQEQLEDSKELQP..SHQETS.GAL..L.RQFQRRLPLRAVNL.L.AGPSWK
Retrocopy MAS*WQGMGASVRRKSLQHQEQLEDSKELQPLASHQETSTGALSTLSRQFQRRLPLRAVNLSLQAGPSWK

Parental  RLETPEPGQQGLQAAARSAKSALGAVSQRIQESCQSGTKWLVETQVKARRRKRGAQK-GSGSPTHSLSQK
          RLETPEPG.QGLQAAA.SAKSALGA.SQRIQESCQS.T.WLVETQVKARRRKRGAQ..GSGSPTHS.S..
Retrocopy RLETPEPGPQGLQAAAPSAKSALGAKSQRIQESCQSSTEWLVETQVKARRRKRGAQR<GSGSPTHSRSHE

Parental  STRLSGAAPAHSAADPWEKEHYRLSA-RMGSRAHPLRRSRREAAFRSPYSSTEPLCSPSESDSDLEPVGA
          STRLSGAAPAHSAADPWEKEH..LSA...GSRAHP.R.SRREAAFRSPYSS.EPLCSPSESDSD....GA
Retrocopy STRLSGAAPAHSAADPWEKEHHHLSA<PIGSRAHPVRLSRREAAFRSPYSSEEPLCSPSESDSDRGTAGA

Parental  GIQHLQKLSQELDEAIMAEESGDI-VSLIHD
          G.QHLQKLSQELDEAIMAEESGD..VSLIHD
Retrocopy GTQHLQKLSQELDEAIMAEESGDMTVSLIHD

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	1.29 RPM
SRP007412_cerebellum	0.00 RPM	2.72 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.29 RPM
SRP007412_liver	0.00 RPM	0.37 RPM
SRP007412_testis	0.00 RPM	0.41 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_2109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2109 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2545

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006997	1 retrocopy	retro_amel_1136,
Homo sapiens	ENSG00000129195	3 retrocopies	retro_hsap_2371, retro_hsap_3030, retro_hsap_3071,
Gorilla gorilla	ENSGGOG00000012309	3 retrocopies	retro_ggor_1801, retro_ggor_2091, retro_ggor_2109 ,
Macaca mulatta	ENSMMUG00000017760	3 retrocopies	retro_mmul_1778, retro_mmul_1935, retro_mmul_959,
Mus musculus	ENSMUSG00000020808	1 retrocopy	retro_mmus_3385,
Nomascus leucogenys	ENSNLEG00000009164	3 retrocopies	retro_nleu_361, retro_nleu_725, retro_nleu_843,
Otolemur garnettii	ENSOGAG00000027433	1 retrocopy	retro_ogar_1490,
Pongo abelii	ENSPPYG00000007877	3 retrocopies	retro_pabe_2141, retro_pabe_2509, retro_pabe_2545,
Pan troglodytes	ENSPTRG00000008641	3 retrocopies	retro_ptro_1734, retro_ptro_2044, retro_ptro_2070,
Rattus norvegicus	ENSRNOG00000008040	1 retrocopy	retro_rnor_1325,