RetrogeneDB ID: retro_pabe_1953

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:50171204..50171929(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP1B3
• Ensembl ID: ENSPPYG00000014169
• Aliases: None
• Description: ATPase, Na+/K+ transporting, beta 3 polypeptide [Source:HGNC Symbol;Acc:806]

Sequence

>retro_pabe_1953
TTAATCTTGCTCTTCTACCTAGTTTTTTATGGGTTCCTGGCTGCACTCTTCTCATTCACGATGTGGGTTATGCTTCAGAC
TCTCAACGATGAGGTTCCAAAATACCGTGACTAGATTCCTAGCCCAGGACTTATGGTTTTTCCAAAACCAGTGATTGCAT
TGGAATATACATTCAGTAGATCTGATCCAACTTCGTATGCAGGGTACACCGAAGACCTTAAGAAGTTTCTAAAACCATAT
ACTTTAGAAGAACAGAAGAACCTCACAGTCTGTTCTGATGGAGCACTTTTTGAACAGAAGGATCCAGTTTATGTTGCATG
TCATTTCCTATTTTGTTACTTCAAGCATGCAGTGGTATGAATGATCCTGATTTTGGCTATTCTCAAGGAAACCCTTGTAT
GCTTGTGAAAATGAACAGAATAATTGGATTAAAGCCTGAAGGAGTGCCAAGGATAGATTGTGTTTCGAAGAGTGAAGATA
TACCAAATGTAGCAGTTTATCCTCATGATGGAATTATAGACTTAAAATATTTCCCATATTATGGGAAAAAACTGCATGTG
GGATATCTACAGCCATTGGTTGCTGTTCAGGTCAGCTTTGCTTCTAACAATACTGGGAAAGAAGTAACAGTTGAGTGCAA
GATTGATCGATCAGCCAGCCTAAAAAGTCAGGATGATTGTGACAAGTTTTTGGGACGAGTTATGTTCAAAATCACAGCAT
GTGCA

Alignment

ORF - retro_pabe_1953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.18 %
• Parental protein coverage: 91.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LILLFYLVFYGFLAALFSFTMWVMLQTLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSRSDPTSYAGYI
          LILLFYLVFYGFLAALFSFTMWVMLQTLNDEVPKYRD.IPSPGLMVFPKPV.ALEYTFSRSDPTSYAGY.
Retrocopy LILLFYLVFYGFLAALFSFTMWVMLQTLNDEVPKYRD*IPSPGLMVFPKPVIALEYTFSRSDPTSYAGYT

Parental  EDLKKFLKPYTLEEQKNLTVCPDGALFEQKGPVYVACQF-PVSLLQACSGMNDPDFGYSQGNPCILVKMN
          EDLKKFLKPYTLEEQKNLTVC.DGALFEQK.PVYVAC.F.P..LLQACSGMNDPDFGYSQGNPC.LVKMN
Retrocopy EDLKKFLKPYTLEEQKNLTVCSDGALFEQKDPVYVACHF<PILLLQACSGMNDPDFGYSQGNPCMLVKMN

Parental  RIIGLKPEGVPRIDCVSKNEDIPNVAVYPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVSFAPNNTGKEV
          RIIGLKPEGVPRIDCVSK.EDIPNVAVYPH.G.IDLKYFPYYGKKLHVGYLQPLVAVQVSFA.NNTGKEV
Retrocopy RIIGLKPEGVPRIDCVSKSEDIPNVAVYPHDGIIDLKYFPYYGKKLHVGYLQPLVAVQVSFASNNTGKEV

Parental  TIECKIDGSANLKSQDDRDKFLGRVMFKITARA
          T.ECKID.SA.LKSQDD.DKFLGRVMFKITA.A
Retrocopy TVECKIDRSASLKSQDDCDKFLGRVMFKITACA

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	1.94 RPM	53.08 RPM
SRP007412_cerebellum	1.58 RPM	93.75 RPM
SRP007412_heart	0.24 RPM	23.69 RPM
SRP007412_kidney	0.80 RPM	28.24 RPM
SRP007412_liver	0.31 RPM	14.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1953 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1953 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2263
Pan troglodytes	retro_ptro_1603

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014140	5 retrocopies	retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni	ENSCHOG00000007515	4 retrocopies	retro_chof_1000, retro_chof_1421, retro_chof_2393, retro_chof_2445,
Callithrix jacchus	ENSCJAG00000001981	1 retrocopy	retro_cjac_309,
Cavia porcellus	ENSCPOG00000003739	4 retrocopies	retro_cpor_1181, retro_cpor_1468, retro_cpor_1506, retro_cpor_222,
Equus caballus	ENSECAG00000019885	2 retrocopies	retro_ecab_1084, retro_ecab_468,
Loxodonta africana	ENSLAFG00000010553	1 retrocopy	retro_lafr_815,
Mus musculus	ENSMUSG00000032412	2 retrocopies	retro_mmus_2174, retro_mmus_3427,
Nomascus leucogenys	ENSNLEG00000004663	1 retrocopy	retro_nleu_1286,
Otolemur garnettii	ENSOGAG00000008662	1 retrocopy	retro_ogar_2284,
Procavia capensis	ENSPCAG00000013927	1 retrocopy	retro_pcap_350,
Pongo abelii	ENSPPYG00000014169	1 retrocopy	retro_pabe_1953 ,
Rattus norvegicus	ENSRNOG00000011501	2 retrocopies	retro_rnor_2571, retro_rnor_789,
Sus scrofa	ENSSSCG00000011676	3 retrocopies	retro_sscr_889, retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus	ENSSTOG00000013235	1 retrocopy	retro_itri_1663,
Tupaia belangeri	ENSTBEG00000001004	1 retrocopy	retro_tbel_3620,
Tarsius syrichta	ENSTSYG00000000222	1 retrocopy	retro_tsyr_330,
Tursiops truncatus	ENSTTRG00000012038	1 retrocopy	retro_ttru_333,