RetrogeneDB ID: retro_pabe_2509

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:27172150..27172861(-)
• Located in intron of: ENSPPYG00000014655

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM64A
• Ensembl ID: ENSPPYG00000007877
• Aliases: None
• Description: family with sequence similarity 64, member A [Source:HGNC Symbol;Acc:25483]

Sequence

>retro_pabe_2509
ATGGCTTCTCGGTGGCAGGGTGTAGGGGCCTCTGTGCGCTGGAGAACTCTCCAGTACCAGGAACAGCTCAAGGACAACAA
GGAGCTGCAGCCTGTGGCCAGCCATCCAGGAGACCCCTGCCGCAGCCCTGGGTTCCCTGTGCAGACAGTTCCAAAGGAGG
CTGCCCCTGACAGCCGTCAACCTCAATCTCTGGGGAGACCCCTCCTGCAAACACTTGGAAACCCCTGAGCCAGGGCAGCA
GAGCCTCCAGGCTGCAGCTCGCTCAGCTAAGAGTACCTCAGGTGCCAAGTCCCAGAGAATCCAGGAGTCCTGACACCAAG
TGGCTAGTGGAGACTCAGGTGAAGGCCAGGAGGAGGAAGAGAGGGGAACAGAAGAGCAGTGGATCCCCGGCTCACAGCCT
GAGCCAGAAGAGCACCCAGCTGTCTGGAGGCGCCCGTGTCCACTCAGCCGCAGACCCCTGGGAGAAGGAGCATCACTGCC
TCTCTGCCCGGATGGGTTCACGTACCCACCCACTACGGCGGTTGAGGCGGGAGTCTGCCTTCTAGAGCCCCTTACCCCTT
GACAGAGCCCCTCTGCTCTCCCAGTGAGTCTGACAACGACCTAGAGCCTGTGGAGGCAGAAATTCAGCATCTCCAGAAGC
TGTCCCAAGAGCTGGACGAAGCCATTATGGCAGAAGAGAGTGGTGACATGAGCGTCTCTCTCATTCATGAC

Alignment

ORF - retro_pabe_2509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASRWQSMGTSVHRRSLQHQEQLEDSKELQPVVGH-QETSAGALGSLCRQFQRRLPLRAVNLNLRAGPSW
          MASRWQ..G.SV..R.LQ.QEQL.D.KELQPV..H.QET.A.ALGSLCRQFQRRLPL.AVNLNL...PS.
Retrocopy MASRWQGVGASVRWRTLQYQEQLKDNKELQPVASH>QETPAAALGSLCRQFQRRLPLTAVNLNLWGDPSC

Parental  KRLETPEPGQQGLQAAARSAKSALGAVSQRIQ-ESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ
          K.LETPEPGQQ.LQAA...A.SA........Q.ES....TKWLVETQVKARRRKRG.QK.SGSP.HSLSQ
Retrocopy KHLETPEPGQQSLQAA---ARSAKSTSGAKSQ>ESRSPDTKWLVETQVKARRRKRGEQKSSGSPAHSLSQ

Parental  KSTRLSVAAPAHSAADPWEKEHHHLSARMGLRAHPLRRSRREAAF-RSPYSSTEPLCSPSESDSDLEPVG
          KST.LS..A..HSAADPWEKEHH.LSARMG.R.HPLRR.RRE.AF.R.PY..TEPLCSPSESD.DLEPV.
Retrocopy KSTQLSGGARVHSAADPWEKEHHCLSARMGSRTHPLRRLRRESAF>RAPYPLTEPLCSPSESDNDLEPVE

Parental  AGIQHLQKLSQELDEAIMAEESGDI-VYLIHD
          A.IQHLQKLSQELDEAIMAEESGD..V.LIHD
Retrocopy AEIQHLQKLSQELDEAIMAEESGDMSVSLIHD

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	0.06 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.24 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2509 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2509 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2509 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3030
Pan troglodytes	retro_ptro_2044
Gorilla gorilla	retro_ggor_2091
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,