RetrogeneDB ID: retro_btau_647

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:45769458..45769989(-)
• Located in intron of: ENSBTAG00000018272

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSBTAG00000019603
• Aliases: None
• Description: L-lactate dehydrogenase B chain [Source:UniProtKB/Swiss-Prot;Acc:Q5E9B1]

Sequence

>retro_btau_647
ATGGCAACTCTTACGGAAAAACTGATTGCACCAGTTGCAGAAGAAGAGGGAACGGTTCCAAACAATAAGATCACTGTAGA
GGGTACTGGACAAGTCAGTATGGTATTTACCATCAGCATTCTGGGAAAGTCTCTGACTGATGAGTTTGCTCTTGTGGATG
TTTTGGAAGATAAACTCAAAGGAGAAATGATGGACCTGCAGCACAAGAGCTTATTCCTTCAGACACCAAAAATCGTGGCA
GACAAAGATTACTCTGTCACTGCCAATTCCAAGATCGTGGTGTTAAGTGCAAGAGTTCACTAGTAAGAGGGGGAGAGGCA
CCTGAATCTGGTGCAAAAGAACATTAATGTCTTCAAGCTCATCACTGCTCAGATTGTGAAGTACAATCCCAACTACATCA
TCATTGTGGTTTCCAACCTAGCAGACATTCTCACATACATTACCTGGAAACCAAGTGGATTACCCAAGCACTGTGTGATT
GCAAGTGGATGTAATCTGGATTCTGCTATATTTCGCTGTCTTATGGCTGAA

Alignment

ORF - retro_btau_647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.66 %
• Parental protein coverage: 52.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATLKEKLIAPVAEEETRIPNNKITVVGVGQVGMACAISILGKSLTDELALVDVLEDKLKGEMMDLQHGS
          MATL.EKLIAPVAEEE...PNNKITV.G.GQV.M...ISILGKSLTDE.ALVDVLEDKLKGEMMDLQH.S
Retrocopy MATLTEKLIAPVAEEEGTVPNNKITVEGTGQVSMVFTISILGKSLTDEFALVDVLEDKLKGEMMDLQHKS

Parental  LFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP
          LFLQTPKIVADKDYSVTANSKIVV..A.V...EGE..LNLVQ.N.NVFK.I..QIVKY.P..IIIVVSN.
Retrocopy LFLQTPKIVADKDYSVTANSKIVVLSARVH**EGERHLNLVQKNINVFKLITAQIVKYNPNYIIIVVSNL

Parental  VDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAE
          .DILTY.TWK.SGLPKH.VI.SGCNLDSA.FR.LMAE
Retrocopy ADILTYITWKPSGLPKHCVIASGCNLDSAIFRCLMAE

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	0.07 RPM	127.25 RPM
ERP005899_muscle	0.21 RPM	96.87 RPM
SRP017611_brain	0.05 RPM	243.01 RPM
SRP017611_kidney	0.00 RPM	692.59 RPM
SRP017611_liver	0.00 RPM	344.24 RPM
SRP030211_testis	0.00 RPM	38.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_647 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_647 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_647 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Bos taurus	ENSBTAG00000008683	2 retrocopies	retro_btau_1715, retro_btau_1822,
Bos taurus	ENSBTAG00000019603	4 retrocopies	retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647 ,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Oryctolagus cuniculus	ENSOCUG00000022015	1 retrocopy	retro_ocun_805,
Sorex araneus	ENSSARG00000002565	1 retrocopy	retro_sara_713,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Ictidomys tridecemlineatus	ENSSTOG00000022058	2 retrocopies	retro_itri_501, retro_itri_648,