RetrogeneDB ID: retro_ptro_1734

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:207105966..207106676(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM64A
• Ensembl ID: ENSPTRG00000008641
• Aliases: None
• Description: family with sequence similarity 64, member A [Source:HGNC Symbol;Acc:25483]

Sequence

>retro_ptro_1734
ATGGCTTCTTGGTGGCAGAGAATGGGGACCTCCGTGCACCGGAGATGTCTCCAGCACCAGGAGCAGCTGGAGGACGCAAG
GAGCTGCAGCCCGTGACCAGCCATCAGGAGAACTCCGCGGGTCCCTGGGGTCCCTGTGCAGACAGTTCCAATGGAGGCTG
CCTCTGAGAGCCATCAACCTCAACTTCCGTGCAGGCCCTTCCTGCAAATGCTTGGAAACCCCAGAGCCAGGGCAGCAGGG
CCTCCAGGCTACGGCTCACTCAGCTAAGAGTGCCTTGGGTGCCATGCCCCAGAGAATCCAGGAGTCCTGCCAAAGTGGCA
CCAAGTGGCTGGTGGAGACCCAGGTGAAGGCCAGGAGGAGGAAGAGAGGGGCCCAGAAGGGCAGTGGATCCCCAACTCAC
AGCCTGAGCCAGAAGAGCACCCGGCTGTCTGGAGATGCCCCTGCCCACTCAGCCCACAGACCCCTGGGAGAAGGAGCATA
ACTGCCTCTCTGCCCGGATAGGCTCCCATGCCTACCCATTATGACAGTCGACGCGGGAGGCTGCCTTCTGGAGCCCCTAC
TCCTCAGCAGAGCCCCTCTGCTCTCCCAGCCAGTCTGGCAGTGACCTAGAGCCTATGGGGGTGGGAATTCAGCATCTCCA
GAAGCTGTCCCAAGAGCTAGATGAAGCCATTATGGCGGAAGAGAGTGGTGACATCATCTCTCTCATTCAT

Alignment

ORF - retro_ptro_1734 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  MASRWQSMGTSVHRRSLQHQEQLKDS-KELQPVVSHQETSVG-ALGSLCRQFQRRLPLRAVNLNLRAGPS
          MAS.WQ.MGTSVHRR.LQHQEQL.D..KELQPV.SHQE.S.G..LGSLCRQFQ.RLPLRA.NLN.RAGPS
Retrocopy MASWWQRMGTSVHRRCLQHQEQLEDA<KELQPVTSHQENSAG<SLGSLCRQFQWRLPLRAINLNFRAGPS

Parental  WKRLETPEPGQQGLQAAARSAKSALGAVSQRIQESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ
          .K.LETPEPGQQGLQA.A.SAKSALGA..QRIQESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ
Retrocopy CKCLETPEPGQQGLQATAHSAKSALGAMPQRIQESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ

Parental  KSTRLSGATPAHSA-ADPWEKEHHRLSARMGSRAHPLRRSRREAAFRSPYSSTEPLCSPSESDSDLEPVG
          KSTRLSG..PAHSA..DPWEKEH..LSAR.GS.A.PL..S.REAAF.SPYSS.EPLCSPS.S.SDLEP.G
Retrocopy KSTRLSGDAPAHSA>TDPWEKEHNCLSARIGSHAYPL*QSTREAAFWSPYSSAEPLCSPSQSGSDLEPMG

Parental  VGIQHLQKLSQELDEAIMAEESGDVVSLIH
          VGIQHLQKLSQELDEAIMAEESGD..SLIH
Retrocopy VGIQHLQKLSQELDEAIMAEESGDIISLIH

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	0.11 RPM	0.09 RPM
SRP007412_cerebellum	0.07 RPM	0.57 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.16 RPM
SRP007412_liver	0.03 RPM	0.69 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1734 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1734 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1734 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2371
Gorilla gorilla	retro_ggor_1801
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,