RetrogeneDB ID: retro_btau_308

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:107645478..107646282(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.49277
• Ensembl ID: ENSBTAG00000021746
• Aliases: None
• Description: annexin A5 [Source:RefSeq peptide;Acc:NP_001035567]

Sequence

>retro_btau_308
ATGGCACAGGTTCTCAGAGGCACCGTGACTGACTTCCCTGGATTCGATGAGCAGGCCGATGCAGAAACTCTCTGGAAGGC
CATGAAAGGCCTGGGCACGGATGAGGAGAGCATCCTGACTCTGTTGACATCCCGCAGTAATGCTCAGCGCCAGGAGATTG
CTGTGGCTTTTAAAACTCTGTTTGGCAGGGACCTTCTGGATGACCTGAAATCAGAACTGACTGGAAAATTTGAAAAATTA
ATCGTGGCTCTGATGAAACCCTCTCGGCTTTATGATGCCTATGAACTGAAGCATGCTCTTAAGGGATCTGGGACAGATGA
AAAAGTCCTGACAGAAATTATTGCGTCAAGGACACCTGAAGAACTGAGAGCCATAAAACAAGTTTATGAAGAAGAGTATG
GCTCGAGCCTGGAAGATGATGTGGTGGGGGATACTTCAGGGTACTACCAGAGGATGTTGGTGGTTCTCCTTCAGGCTAAT
AGAGACCCTGACGCTAGAATTGATGAAGCACAGGTTGAACAAGACGCTCAGGCTTTGTTCCAGGCTGGAGAACTGAAATG
GGGAACAGATGAATAAAAGTTTATTACCATCTTTGGAACACGAAGTCTATCTCACTTGAGAAGAGTGTTTGACAAATACA
TGACTATATCCGGGTTTCATATTGAAGAAACCATTGACCGGGAGACTTCCGGCAATTTGGAACAGCTTCTCCTTGCTGTT
GTGAAATCCATTCGCAGTATACCTGCCTACCTTGCAGAAACCCTCTACTATGCTATGAAGGGAGCTGGAACAGATGATCA
GAGT

Alignment

ORF - retro_btau_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.27 %
• Parental protein coverage: 83.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQVLRGTVADFPGFDERADAETLRKAMKGLGTDEESILTLLTSRSNAQRQEIAVAFKTLFGRDLLDDLK
          MAQVLRGTV.DFPGFDE.ADAETL.KAMKGLGTDEESILTLLTSRSNAQRQEIAVAFKTLFGRDLLDDLK
Retrocopy MAQVLRGTVTDFPGFDEQADAETLWKAMKGLGTDEESILTLLTSRSNAQRQEIAVAFKTLFGRDLLDDLK

Parental  SELTGKFEKLIVALMKPSRLYDAYELKHALKGAGTDEKVLTEIIASRTPEELRAIEQVYEEEYGSSLEDD
          SELTGKFEKLIVALMKPSRLYDAYELKHALKG.GTDEKVLTEIIASRTPEELRAI.QVYEEEYGSSLEDD
Retrocopy SELTGKFEKLIVALMKPSRLYDAYELKHALKGSGTDEKVLTEIIASRTPEELRAIKQVYEEEYGSSLEDD

Parental  VVGDTSGYYQRMLVVLLQANRDPDARIDEAQVEQDAQALFQAGELKWGTDEEKFITIFGTRSVSHLRRVF
          VVGDTSGYYQRMLVVLLQANRDPDARIDEAQVEQDAQALFQAGELKWGTDE.KFITIFGTRS.SHLRRVF
Retrocopy VVGDTSGYYQRMLVVLLQANRDPDARIDEAQVEQDAQALFQAGELKWGTDE*KFITIFGTRSLSHLRRVF

Parental  DKYMTISGFQIEETIDRETSGNLEQLLLAVVKSIRSIPAYLAETLYYAMKGAGTDDHT
          DKYMTISGF.IEETIDRETSGNLEQLLLAVVKSIRSIPAYLAETLYYAMKGAGTDD..
Retrocopy DKYMTISGFHIEETIDRETSGNLEQLLLAVVKSIRSIPAYLAETLYYAMKGAGTDDQS

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	0.14 RPM	19.61 RPM
ERP005899_muscle	0.90 RPM	233.38 RPM
SRP017611_brain	1.87 RPM	124.07 RPM
SRP017611_kidney	2.49 RPM	210.47 RPM
SRP017611_liver	0.08 RPM	8.76 RPM
SRP030211_testis	0.08 RPM	20.84 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_308 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_308 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009615	2 retrocopies	retro_btau_634, retro_btau_985,
Bos taurus	ENSBTAG00000015978	1 retrocopy	retro_btau_544,
Bos taurus	ENSBTAG00000021746	1 retrocopy	retro_btau_308 ,
Echinops telfairi	ENSETEG00000002187	3 retrocopies	retro_etel_1728, retro_etel_370, retro_etel_901,
Macropus eugenii	ENSMEUG00000003853	3 retrocopies	retro_meug_1071, retro_meug_1782, retro_meug_985,
Otolemur garnettii	ENSOGAG00000003878	1 retrocopy	retro_ogar_2257,