RetrogeneDB ID: retro_ptro_1603

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:61584215..61585048(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP1B3
• Ensembl ID: ENSPTRG00000015476
• Aliases: None
• Description: ATPase, Na+/K+ transporting, beta 3 polypeptide [Source:HGNC Symbol;Acc:806]

Sequence

>retro_ptro_1603
ACGATGAAGAAGAACGAGTCCCTCAACCAGAGCCTCGCCGAGTGGAAGCTCTTCATCTACAACCCGACCACCGGAGAGTT
CCTGGGGCGCACCGCCAAGAGCTGGGGTTTGATGTTGCTCTTCTACCTAATTTTTTATGGGTTCCTGGCTGCACTCTTCT
TATTCACGATGTGGGTTATGCTTCAGACTCAACGATGAGCTTCTAAAATACCGTGACCAGATTCTTAACCCAGGACTTAT
GGTTTTTCCAAAACCAGTGACTGCATTGGAATATACATTCAGTAGGTCTGATCTAACTTCGTATGCAGGGTACACTGAAG
ACCTTAAGAAGTTTCTAAAACCATATACTTTAGAAGAACAGAAAAACCTCACAGGCTGTCCTGATGGAGCACTTTTTGAA
CAGAAGGGTCCAGTTTATGTTGTATGTCAGTTTCCCATTTCGTTACTTCAAGCATGCCGTGGTATGAATGATCTTGATTT
CAGCTATTCTCAAAGAAACCCTTGTATTCTTGTGAAAATGAACAGAATAATTGGATTAAAGTCTGAAGGAGTGCCAAGGA
TAGATTGTGTTTCGAAGAATGAAGATATACCAAATGTAGCAGTTTATCCTCATAATGGAATTATAGACTTAAAATATTTC
CCATATTATGGGGAAAAACTGCATGTGGGGTATCTACAGCCATTGGTTGCTGTTCAGGTCAGCTTTGCTCCTAACGATAC
TGAGAAAGAAGTTAACAGCTGAGTGCAAGATTGATGGATCAGCCAACCTTAAAAGTCAGGATGATCGTGACAAGTTTTTG
GGACGAGTTATGTTCAAAATCACAGCATGTGCA

Alignment

ORF - retro_ptro_1603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.79 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TKNEKKSLNQSLAEWKLFIYNPTTGEFRGRTAKSWGLILLFYLVFYGFLAALF-SFTMWVMLQTLNDEVP
          T.....SLNQSLAEWKLFIYNPTTGEF.GRTAKSWG...L..........A...S.........LNDE..
Retrocopy TMKKNESLNQSLAEWKLFIYNPTTGEFLGRTAKSWG-LMLLFYLIFYGFLAAL>SYSRCGLCFRLNDELL

Parental  KYRDQIPSPGLMVFPKPVTALEYTFSRSDPTSYAGYIEDLKKFLKPYTLEEQKNLTVCPDGALFEQKGPV
          KYRDQI..PGLMVFPKPVTALEYTFSRSD.TSYAGY.EDLKKFLKPYTLEEQKNLT.CPDGALFEQKGPV
Retrocopy KYRDQILNPGLMVFPKPVTALEYTFSRSDLTSYAGYTEDLKKFLKPYTLEEQKNLTGCPDGALFEQKGPV

Parental  YVACQFPISLLQACSGMNDPDFGYSQGNPCILVKMNRIIGLKPEGVPRIDCVSKNEDIPNVAVYPHNGMI
          YV.CQFPISLLQAC.GMND.DF.YSQ.NPCILVKMNRIIGLK.EGVPRIDCVSKNEDIPNVAVYPHNG.I
Retrocopy YVVCQFPISLLQACRGMNDLDFSYSQRNPCILVKMNRIIGLKSEGVPRIDCVSKNEDIPNVAVYPHNGII

Parental  DLKYFPYYGKKLHVGYLQPLVAVQVSFAPNNTGKEV-TVECKIDGSANLKSQDDRDKFLGRVMFKITARA
          DLKYFPYYG.KLHVGYLQPLVAVQVSFAPN.T.KEV.T.ECKIDGSANLKSQDDRDKFLGRVMFKITA.A
Retrocopy DLKYFPYYGEKLHVGYLQPLVAVQVSFAPNDTEKEV>TAECKIDGSANLKSQDDRDKFLGRVMFKITACA

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	0.04 RPM	54.89 RPM
SRP007412_cerebellum	0.00 RPM	46.24 RPM
SRP007412_heart	0.03 RPM	15.01 RPM
SRP007412_kidney	0.00 RPM	30.75 RPM
SRP007412_liver	0.00 RPM	18.13 RPM
SRP007412_testis	0.11 RPM	86.41 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1603 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1603 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1603 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2263
Pongo abelii	retro_pabe_1953

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 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,
Homo sapiens	ENSG00000069849	2 retrocopies	retro_hsap_1387, retro_hsap_2263,
Loxodonta africana	ENSLAFG00000010553	1 retrocopy	retro_lafr_815,
Mus musculus	ENSMUSG00000032412	2 retrocopies	retro_mmus_2174, retro_mmus_3427,
Otolemur garnettii	ENSOGAG00000008662	1 retrocopy	retro_ogar_2284,
Procavia capensis	ENSPCAG00000013927	1 retrocopy	retro_pcap_350,
Pan troglodytes	ENSPTRG00000001653	1 retrocopy	retro_ptro_1979,
Pan troglodytes	ENSPTRG00000015476	2 retrocopies	retro_ptro_1603 , retro_ptro_951,
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,