RetrogeneDB ID: retro_pabe_456

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:151031987..151032541(-)
• Located in intron of: ENSPPYG00000001217

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR3
• Ensembl ID: ENSPPYG00000014233
• Aliases: None
• Description: Translocon-associated protein subunit gamma [Source:UniProtKB/Swiss-Prot;Acc:Q5RCD7]

Sequence

>retro_pabe_456
ATGGCTCCCTAAGGCAGCTCCAAACAGCCGTCCGAGGAGGACCCGCTCCTGCAGGATTTCAGCGGCAACCTCTCGGCCAA
GTCCTTCGCAGTCTTCTTCGGGAATGCGTTCGTCGTGTCTGCCATCCCCATCTGGTTATACTAGAGAATATGGCATATGG
ATCTTATTCAGTCTGCTGTTTTCTATAGTGTGATGACCCTAGAAAGCACGTATTTGGTAGCCTTTGCATACAAGAATGTT
AAATTTGTTCTCAAGCACAAAGTAGCACAGAAGAGGGAGGATGCTGTTTCCAAAGAATTGACTCGAAAACTTTCTGAAGC
TGATAATAGAAAGATGTCTCGGAAGGAGAAAGATGTAAGAATCTTGTGGAAGAAGAGTGAAGTTGCTGATTCTGAAGCTA
CAACATTTTCCATCTTCTATAACAACACTCTGTTCCTGGTCTTGGTCATTGTTGCTGCTTCTTCATTTTGAAGAACTTCA
ACCCCACAGTGAACTACATTTTGTCCATAAGTGCTTCATCAGGACTCATCGCCCTCCTGTCTACTGGCTCCAAG

Alignment

ORF - retro_pabe_456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPKGSCKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAVLYSVMTLVST
          MAP.GS.KQ.SEED.LLQDFS.NLSAKS.A.FFGNAF.VSAIPIWLY.RIWHMDLIQSAV.YSVMTL.ST
Retrocopy MAP*GSSKQPSEEDPLLQDFSGNLSAKSFAVFFGNAFVVSAIPIWLY*RIWHMDLIQSAVFYSVMTLEST

Parental  YLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFY
          YLVAFAYKNVKFVLKHKVAQKREDAVSKE.TRKLSEADNRKMSRKEKD.RILWKK.EVAD.EATTFSIFY
Retrocopy YLVAFAYKNVKFVLKHKVAQKREDAVSKELTRKLSEADNRKMSRKEKDVRILWKKSEVADSEATTFSIFY

Parental  NNTLFLVVVIVAS-FFILKNFNPTVNYILSISASSGLIALLSTGSK
          NNTLFLV.VIVA..FFILKNFNPTVNYILSISASSGLIALLSTGSK
Retrocopy NNTLFLVLVIVAA<FFILKNFNPTVNYILSISASSGLIALLSTGSK

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	0.06 RPM	31.68 RPM
SRP007412_cerebellum	0.00 RPM	33.68 RPM
SRP007412_heart	0.12 RPM	60.21 RPM
SRP007412_kidney	0.07 RPM	38.38 RPM
SRP007412_liver	0.03 RPM	55.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_456 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_456 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_456 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_173
Pan troglodytes	retro_ptro_163
Gorilla gorilla	retro_ggor_255
Macaca mulatta	retro_mmul_383

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003125	1 retrocopy	retro_amel_832,
Canis familiaris	ENSCAFG00000008870	5 retrocopies	retro_cfam_1296, retro_cfam_1370, retro_cfam_1924, retro_cfam_2029, retro_cfam_2041,
Choloepus hoffmanni	ENSCHOG00000001517	1 retrocopy	retro_chof_29,
Callithrix jacchus	ENSCJAG00000004643	4 retrocopies	retro_cjac_1059, retro_cjac_1503, retro_cjac_2369, retro_cjac_3213,
Cavia porcellus	ENSCPOG00000005898	2 retrocopies	retro_cpor_1243, retro_cpor_826,
Dasypus novemcinctus	ENSDNOG00000000752	2 retrocopies	retro_dnov_1922, retro_dnov_632,
Homo sapiens	ENSG00000114850	1 retrocopy	retro_hsap_173,
Gorilla gorilla	ENSGGOG00000024038	1 retrocopy	retro_ggor_255,
Myotis lucifugus	ENSMLUG00000015478	3 retrocopies	retro_mluc_1624, retro_mluc_1728, retro_mluc_2146,
Macaca mulatta	ENSMMUG00000016970	1 retrocopy	retro_mmul_383,
Otolemur garnettii	ENSOGAG00000010589	2 retrocopies	retro_ogar_2089, retro_ogar_3483,
Pongo abelii	ENSPPYG00000014233	1 retrocopy	retro_pabe_456 ,
Pan troglodytes	ENSPTRG00000015560	1 retrocopy	retro_ptro_163,
Tarsius syrichta	ENSTSYG00000010578	1 retrocopy	retro_tsyr_660,