RetrogeneDB ID: retro_btau_210

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:20415892..20416639(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000038232
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSBTAG00000033217
• Aliases: None
• Description: Tropomyosin alpha-3 chain [Source:UniProtKB/Swiss-Prot;Acc:Q5KR47]

Sequence

>retro_btau_210
ATGGCCGCGATCGCTGTCACCGAGGCAATGAAGTGCAAGATCCAGGTTCTGCAGCAGCAGGCCGATGATGCAGAGGAGAG
GGCCAAGCGCCTCCAGCAGAAAGTGGATGGAGAAAGATGGGCCCGAGAACAGGCTGAGGCTGAAGTGGTCTCCTTAAACC
GTAGGATCCAGCTGGTTGAAGAGGAGCTGAACCGAGCTCAAGAGCGCCTGGCCACTGCGCTGCAAAAGCTGGAGGAAGCT
GAGAAAGCTGCTGATGAGAGCGAGAGAGTTATGAAGGTTATTGAAAACCAAGCCTTAAAAGATGAAGAAAAAATGGAACT
CCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCACACAGGAAGTATGAAGAGGTGGCTCGCAAGTTGG
TGATTATTGAGGGAGACTTGGAGCGCACAGAGGAGCGAGCGGAGCTGGCACAGTCCCGTTGCCGAAAGATGGGTGAGCAA
ATCAGACTGATGGACCAGCACCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAGGAAGACAAATATGAGGA
AGAGATAAAGATTCTTACCGAAAAACTCAAGGAGGCAGAGACTCGTGCTGAGTTTGCTGAGAGATCAGTAGCCAAGCTGG
AAAAGACAATTGATGATTTGGAAGATAAACTGAAATGCACCAAAGAGGAGGACCTCTGTACACAAAGGATGCTGAACCAG
ACTCTGCTTGACCTGAATAAAATGTAG

Alignment

ORF - retro_btau_210 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MA.I...EA.K.KIQVLQQQADDAEERA.RLQ..V.GER.AREQAEAEV.SLNRRIQLVEEEL.RAQERL
Retrocopy MAAIAVTEAMKCKIQVLQQQADDAEERAKRLQQKVDGERWAREQAEAEVVSLNRRIQLVEEELNRAQERL

Parental  ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
          ATALQKLEEAEKAADESER.MKVIEN.ALKDEEKMELQEIQLKEAKHIAEEA.RKYEEVARKLVIIEGDL
Retrocopy ATALQKLEEAEKAADESERVMKVIENQALKDEEKMELQEIQLKEAKHIAEEAHRKYEEVARKLVIIEGDL

Parental  ERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV
          ERTEERAELA.SRCR.M.EQIRLMDQ.LKCLSAAEEKYSQKEDKYEEEIKILT.KLKEAETRAEFAERSV
Retrocopy ERTEERAELAQSRCRKMGEQIRLMDQHLKCLSAAEEKYSQKEDKYEEEIKILTEKLKEAETRAEFAERSV

Parental  AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          AKLEKTIDDLEDKLKCTKEE.LCTQRML.QTLLDLN.M
Retrocopy AKLEKTIDDLEDKLKCTKEEDLCTQRMLNQTLLDLNKM

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	92.57 RPM
ERP005899_muscle	0.00 RPM	401.94 RPM
SRP017611_brain	0.00 RPM	99.40 RPM
SRP017611_kidney	1.36 RPM	134.25 RPM
SRP017611_liver	0.00 RPM	82.08 RPM
SRP030211_testis	0.03 RPM	97.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_210 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_210 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000004553	2 retrocopies	retro_btau_1604, retro_btau_1758,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210 , retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,