RetrogeneDB ID: retro_ptro_2044

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:26849258..26849969(-)
• Located in intron of: ENSPTRG00000015971

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_2044
ATGGCTTCTCAGCGGCAGGGTGTAGGGGCCTCTGTGCGCCGGAGATCTCTCCAGTACCAGGAGCAGCTCAAGAACAGCAA
GGAGCTGCAGCCTGTGGCCAGCCATCCAGGAGACCCCTGCCGCAGCCCTGGGTTCCCTGTGCAGACAGTTCCAAAGGAGG
CTGCCCCTGACAGCCGTCAACCTCAATCTCTGGGGAGACCCCTCCTGCAAACACTTGGAAACCCCAGAGCCAGGGCAGCA
GAGCCTCCAAGCTGCAGCTCGCTCAGCTAAGAGTGCCTCAGGTGCCAAGTCCCAGAGAATCCAGGAGTCCTGACACCAAG
TGGCTGGTGGAGACTCAGGTGAAGGCCAGGAGGAGAAAGAGAGGGGCACAGAAGAGCAGTGGATCCCTGACTCACAGCCT
GAGCCAGAAGAGCACCCAGCTGTCTGGAGGCGCCCCTGTCCACTCAGCCGCAGACCCCTGGGAGAAGAAGCATCACTGCC
TCTCTGCCCGGATGGGTTCACGTACCCACCCACTACGGCGGTTGAGGCGGGAGTCTGCCTTGTAGAGCCCCTTACCCCTT
GACAGAGCCCCTCTGCTCTCCCAGTGAATCTGACAGTGACCTAGAGCCTGTGGAGGCAGAAATTCAGCATCTCCACAAGC
TGTCCCAAGAGCTGGATGAAGCCATTATGGCAGAAGAGAGTGGTGACATGAGCGTCTCTCTCATTCATGAC

Alignment

ORF - retro_ptro_2044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASRWQSMGTSVHRRSLQHQEQLKDSKELQPVVSH-QETSVGALGSLCRQFQRRLPLRAVNLNLRAGPSW
          MAS..Q..G.SV.RRSLQ.QEQLK.SKELQPV.SH.QET...ALGSLCRQFQRRLPL.AVNLNL...PS.
Retrocopy MASQRQGVGASVRRRSLQYQEQLKNSKELQPVASH>QETPAAALGSLCRQFQRRLPLTAVNLNLWGDPSC

Parental  KRLETPEPGQQGLQAAARSAKSALGAVSQRIQ-ESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ
          K.LETPEPGQQ.LQAA...A.SA..A.....Q.ES....TKWLVETQVKARRRKRGAQK.SGS.THSLSQ
Retrocopy KHLETPEPGQQSLQAA---ARSAKSASGAKSQ>ESRSPDTKWLVETQVKARRRKRGAQKSSGSLTHSLSQ

Parental  KSTRLSGATPAHSAADPWEKEHHRLSARMGSRAHPLRRSRREAAF-RSPYSSTEPLCSPSESDSDLEPVG
          KST.LSG..P.HSAADPWEK.HH.LSARMGSR.HPLRR.RRE.A..R.PY..TEPLCSPSESDSDLEPV.
Retrocopy KSTQLSGGAPVHSAADPWEKKHHCLSARMGSRTHPLRRLRRESAL>RAPYPLTEPLCSPSESDSDLEPVE

Parental  VGIQHLQKLSQELDEAIMAEESGDV-VSLIHD
          ..IQHL.KLSQELDEAIMAEESGD..VSLIHD
Retrocopy AEIQHLHKLSQELDEAIMAEESGDMSVSLIHD

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	0.09 RPM
SRP007412_cerebellum	0.18 RPM	0.57 RPM
SRP007412_heart	0.15 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.16 RPM
SRP007412_liver	0.00 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_2044 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2044 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2044 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3030
Gorilla gorilla	retro_ggor_2091
Pongo abelii	retro_pabe_2509
Macaca mulatta	retro_mmul_1935

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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,