RetrogeneDB ID: retro_btau_769

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:50678400..50678660(+)
• Located in intron of: ENSBTAG00000003687

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.43863
• Ensembl ID: ENSBTAG00000021491
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P25712]

Sequence

>retro_btau_769
ATGGTAACCTCCTTTCTACTGTGGCAAAGACGAGCCGGGGTACTGAAGACTGTGCTTCTAGAAGCTGGAGTGTTTCGAGG
ACTTACTCCTACAATTTCTCTTTCTACAGAATCAGGAAAGAATGAAAAGGAATTGCCACCAAATCCCAAGAAGCAAAGTC
CACCAAAAGAGCACACACCAGCCACTGCCTCTGCTGAGGGGTCTGAGAAAGCACCTTTAAGAATCTCCAGCATCAGGATT
ATGGCACATACACCTTCTTA

Alignment

ORF - retro_btau_769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.77 %
• Parental protein coverage: 78.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASLLLRQGRAGALKTVLLEAGVFRGVAPAVSLSAESGKNEKGLPPNPKKQS-PPKKPVSAAPTEPFDN
          M..S.LL.Q.RAG.LKTVLLEAGVFRG..P..SLS.ESGKNEK.LPPNPKKQS.P.......A..E....
Retrocopy MVTSFLLWQRRAGVLKTVLLEAGVFRGLTPTISLSTESGKNEKELPPNPKKQSPPKEHTPATASAEGSEK

Parental  -TTYKNLQHHDYSTYTFL
          ..T.KNLQH.DY.TYTFL
Retrocopy <STFKNLQHQDYGTYTFL

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	11.32 RPM
ERP005899_muscle	0.00 RPM	43.34 RPM
SRP017611_brain	0.00 RPM	41.66 RPM
SRP017611_kidney	0.00 RPM	58.26 RPM
SRP017611_liver	0.00 RPM	23.79 RPM
SRP030211_testis	0.00 RPM	38.40 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_769 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_769 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021491	10 retrocopies	retro_btau_445, retro_btau_769 , retro_btau_770, retro_btau_772, retro_btau_773, retro_btau_774, retro_btau_803, retro_btau_804, retro_btau_805, retro_btau_806,
Canis familiaris	ENSCAFG00000010508	1 retrocopy	retro_cfam_1001,
Callithrix jacchus	ENSCJAG00000015786	1 retrocopy	retro_cjac_1498,