RetrogeneDB ID: retro_btau_1166

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:272263..273007(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046335
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1166
ATGGCCGGGATCCCCACTATCGAGGCGGTGAAGCGCAAGATCCAGGTTCTGCAGCAGCAGGCCGATGATGCACAGGAGAG
GGCCGAGCGCCTCCAGCGGGAAGTGGAGGGAGAAGGACGGGCCCGAGAACAGGCTGAGGCTGAGGTGGCCTCCTTGAACC
GTAGGATCCAGCTGGTCGAAGAGGAGCTGGACCGAGCTCAAGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAGGAAGCT
GAGAAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACCAAGCCTTAAAAGATGAAGAAAAAATGGAACT
CCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAGACAGGAAGTATGAAGAGGTGGCTCGCAAGTTGG
TGATTATTGACGGAGACTTGGAGGGCACAGAGGAGCGAGCCGAGCTGGCAGAGTCCCGTTGCCGAGAGATGGATGAGCAA
ATCAAACTGATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATATAAGGA
AGAGATAAAGATTCTTACCGATAAACTCAAGGAGGCAGAGACCCGTGCTGAATTTGCTGAGAGATTGGTAGCCAAGCTGG
AAAAGACAATTGATGATTTGGAAGATAAACTGAAATGCACCAAAGAGGAGCACCTCTGTACACAAAGGATGTTGGACCAG
ACTCTGCTTGACCTGAATGAGATG

Alignment

ORF - retro_btau_1166 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MAGI.TIEAVKRKIQVLQQQADDA.ERAERLQREVEGE.RAREQAEAEVASLNRRIQLVEEELDRAQERL
Retrocopy MAGIPTIEAVKRKIQVLQQQADDAQERAERLQREVEGEGRAREQAEAEVASLNRRIQLVEEELDRAQERL

Parental  ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
          ATALQKLEEAEKAADESERGMKVIEN.ALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVII.GDL
Retrocopy ATALQKLEEAEKAADESERGMKVIENQALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIDGDL

Parental  ERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV
          E.TEERAELAESRCREMDEQI.LMDQNLKCLSAAEEKYSQKEDKY.EEIKILTDKLKEAETRAEFAER.V
Retrocopy EGTEERAELAESRCREMDEQIKLMDQNLKCLSAAEEKYSQKEDKYKEEIKILTDKLKEAETRAEFAERLV

Parental  AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
Retrocopy AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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	92.57 RPM
ERP005899_muscle	0.32 RPM	401.94 RPM
SRP017611_brain	0.09 RPM	99.40 RPM
SRP017611_kidney	0.18 RPM	134.25 RPM
SRP017611_liver	0.08 RPM	82.08 RPM
SRP030211_testis	0.20 RPM	97.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1166 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1166 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,