RetrogeneDB ID: retro_btau_1743

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:55279500..55279967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP1B3
• Ensembl ID: ENSBTAG00000014140
• Aliases: None
• Description: Sodium/potassium-transporting ATPase subunit beta-3 [Source:UniProtKB/Swiss-Prot;Acc:Q3T0C6]

Sequence

>retro_btau_1743
CCAAAATCAGTGACTGTGTTGGAATATTCATTTAGTTTGTCTGATCCAGACTCCTATAAAGGGTACATTGAAGACCTAAA
GCCATATGACTTGGAAAAATGAAAGAATCTCACAGTTTGCCCTGATGAAGTGCCTTTTGAACAGAGAAGTCCAATTTATG
TTGTATGTCATGTTTCTTATTGCCTTACTTCAAGCATGCAGTGCTGTGGATGATCCTGAGTTTGGCTATATCAGAGGAAA
CCCTTGTATTCATGTGAAAATGAGCAAAGTAATTGGATTAAAGCTTCAAAGAGAATCAACTATAGAATATATTTTGAAGG
ATGAAAACATAGCAACTGTATTAACTTATCTTCCCAATGGAATTAAAATATTTTCCATATTATGAGAAAAAACTGCATAT
GAGGCATCTACAGTCATTAGTTGCCATCTAGATTACCTTTGACCCATGGAGTACTGTCAAAAAGTTA

Alignment

ORF - retro_btau_1743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.83 %
• Parental protein coverage: 58.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKPVSALDFSFSLSDAESYQGYIDDLKKFLKPYGLEEQKNLTDCTNGTFFEQKGPEYTAC-QFPLALLEA
          PK.V..L..SFSLSD..SY.GYI.DLK....PY.LE..KNLT.C.....FEQ..P.Y..C..F..ALL.A
Retrocopy PKSVTVLEYSFSLSDPDSYKGYIEDLK----PYDLEK*KNLTVCPDEVPFEQRSPIYVVC>MFLIALLQA

Parental  CSGVDDPTFGYQEGKPCILVKMNRIIGLKPQGEPRIECTGKSESTAFLSTYPSNGTIDLKYF-PYYGKKL
          CS.VDDP.FGY..G.PCI.VKM...IGLK.Q.E..IE...K.E..A...TY..NG....K.F.PYY.KKL
Retrocopy CSAVDDPEFGYIRGNPCIHVKMSKVIGLKLQRESTIEYILKDENIATVLTYLPNG---IKIF>PYYEKKL

Parental  HGNYLQPLVAVQVGFGSDADVREV
          H...LQ.LVA....F.....V...
Retrocopy HMRHLQSLVAI*ITFDPWSTVKKL

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
ERP005899_liver	0.00 RPM	83.56 RPM
ERP005899_muscle	0.00 RPM	162.80 RPM
SRP017611_brain	0.00 RPM	35.26 RPM
SRP017611_kidney	0.00 RPM	21.34 RPM
SRP017611_liver	0.00 RPM	73.09 RPM
SRP030211_testis	0.00 RPM	135.47 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1743 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1743 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_1084

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 36 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,
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,
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,