RetrogeneDB ID: retro_ggor_1801

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:90834845..90835555(-)
• 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_1801
ATGGCTTCTTGGTGGCAGAGAATGGGGACCTCCGTGCACCGGAGATGTCTCCAGCACCAGGAGCAGCTGGAGGACGCAAG
GAGCTGCAGCCCGTGACCAGCCATCAGGAGAACTCCACGGGTCCCTGGGGTCCCTGTGCAGACAGTTCCAATGGAGGCTG
CCTCTGAGAGCCATCAACCTCAACTTCCGTGCAGGCCCTTCCTGCAAATGCTTGGAAACCCCAGAGCCAGGGCAGCAGGG
CCTCCAGGCTACAGCTCACTCAGCTAAGAGTGCCTTGGGTGCCATGTCCCAGAGAATCCAAGAGTCCTGCCAAAGTGGCA
CCAAGTGGCTGGTGGAGACCCAGGTGAAGGCCAGGAGGAGGAAGAGAGGGGCACAGAAGGGCAGTGGATCCCCAACTCAC
AGCCTGAGCCAGAAGAGCACCCAGCTGTCTGGAGATGTCCCTGCCCACTCAGCCCACAGACCCCTGGGAGAAGGAGCATA
ACTGCCTCTCTGCCCGGATAGGCTCCCATGCCTACCCATTATGACAGTCAATGCGGGAGGCTGCCTTCTGGAGCCCCTAC
TCCTCAACAGAGCCCCTCTGCTCTCCCAGCCAGTCTGGCAGTGACCTAGAGCCTATGGGGGTGGGAATTCAGCATCTCCA
GAAGCTGTCCCAAGAGCTAGATGAAGCCTTTATGGCGGAAGAGAGTGGTGACATCATCTCTCTCATTCAT

Alignment

ORF - retro_ggor_1801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASRWQSMGTSVRRRSLQHQEQLEDS-KELQPVVSHQETSVG-ALGSLCRQFQRRLPLRAVNLNLRAGPS
          MAS.WQ.MGTSV.RR.LQHQEQLED..KELQPV.SHQE.S.G..LGSLCRQFQ.RLPLRA.NLN.RAGPS
Retrocopy MASWWQRMGTSVHRRCLQHQEQLEDA<KELQPVTSHQENSTG<SLGSLCRQFQWRLPLRAINLNFRAGPS

Parental  WKRLETPEPGQQGLQAAARSAKSALGAVSQRIQESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ
          .K.LETPEPGQQGLQA.A.SAKSALGA.SQRIQESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ
Retrocopy CKCLETPEPGQQGLQATAHSAKSALGAMSQRIQESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ

Parental  KSTRLSGAAPAHSA-ADPWEKEHYRLSARMGSRAHPLRRSRREAAFRSPYSSTEPLCSPSESDSDLEPVG
          KST.LSG..PAHSA..DPWEKEH..LSAR.GS.A.PL..S.REAAF.SPYSSTEPLCSPS.S.SDLEP.G
Retrocopy KSTQLSGDVPAHSA>TDPWEKEHNCLSARIGSHAYPL*QSMREAAFWSPYSSTEPLCSPSQSGSDLEPMG

Parental  AGIQHLQKLSQELDEAIMAEESGDIVSLIH
          .GIQHLQKLSQELDEA.MAEESGDI.SLIH
Retrocopy VGIQHLQKLSQELDEAFMAEESGDIISLIH

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	0.10 RPM	1.29 RPM
SRP007412_cerebellum	0.20 RPM	2.72 RPM
SRP007412_heart	0.06 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.29 RPM
SRP007412_liver	0.05 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_1801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1801 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2371
Pan troglodytes	retro_ptro_1734
Pongo abelii	retro_pabe_2141
Macaca mulatta	retro_mmul_959

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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,