RetrogeneDB ID: retro_btau_699

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:45852251..45853041(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.29579
• Ensembl ID: ENSBTAG00000012525
• Aliases: None
• Description: histo-blood group ABO system transferase [Source:RefSeq peptide;Acc:NP_001071394]

Sequence

>retro_btau_699
AGGATGGTGTATTCCCCACCAGATGTGCTTGTACCACCTACGAAAGATGTCCTTCTTATGACCCCCTGGCTGGCTCCCAT
CATCTGGAATGGGACTTTCAACATTGACATCCTGAATGAGCAGTTCCGGCTTCAGAACATCACCATTGGATTAACTGTGT
TTGTTGTAAAAAAAATACATTTTCCACCTGAAGCTCTTCCTGGAGATGGCAGAGATGTACTTTATGGTGGGACACAGGGT
GAACTACTATATCTTCACTGATCGGCCAGACTACGTTCCTCTCATTCGCCTTCAGAGAGGACGGCAGATGGTCATCTTCA
AGGTCCAGAGGTATGCCCACTGGCAGAAGATTTCCACACACCGCATGAAGGTGATCAGCAATTTTATTGAGTAGCGCTTC
CACCAGGAAGTGGATTACCTTGTGTGTGCAAATGTGGACATGAAGTTTAGTGATGATGTGGGCGTGGAGATCCTGTCCTC
CTTGTTCAGCATCCTCCATCCTGGCTTCCATGGATTGACTCGGAAATACTTTGAATATGAACACCAGCTTCCATCACAGG
CCCATATTCCTGAAGATAAGGAGGACTTTTATTACATAGGGGCCTTATTTGGGGAGTCCATGCCAGAGGTTTACAGACTT
GCCAAGGCCTGCCATGAGGCGATGATGGTTGACCAGGCCAATCACATCGAGGCCACATGAAATGATGAGAGCCACCTGAA
CAAATACCTGCTTTATCACAAACCCACCAAGGTCCTTTCCCCTGAGTACATGTGGGATAGTCAAATACTC

Alignment

ORF - retro_btau_699 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.23 %
• Parental protein coverage: 72.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLLYPKAQLLKPLRVDVLVMTPWFAPVVWDGTFDSALLDVQFR--NTTIGLTVFAIKK-YVVFLRLFLET
          R..Y.....L.P...DVL.MTPW.AP..W.GTF....L..QFR..N.TIGLTVF.....Y...L.LFLE.
Retrocopy RMVYSPPDVLVPPTKDVLLMTPWLAPIIWNGTFNIDILNEQFRLQNITIGLTVFVXXX>YIFHLKLFLEM

Parental  AEKYFMVGHKVIYYVFTDRPADVPQIALQDGRQVVVLHVGNYRRWQDISMHRMEMISNFSRRRFLREVDY
          AE.YFMVGH.V.YY.FTDRP..VP.I.LQ.GRQ.V...V..Y..WQ.IS.HRM..ISNF...RF..EVDY
Retrocopy AEMYFMVGHRVNYYIFTDRPDYVPLIRLQRGRQMVIFKVQRYAHWQKISTHRMKVISNFIE*RFHQEVDY

Parental  LVCLYVDMKFSDHVGVEILAPLFGTLHPGFYAADRQSFTYERRPLSRAYIPRDEGDFYYAGGFFGGSVPE
          LVC..VDMKFSD.VGVEIL..LF..LHPGF....R..F.YE....S.A.IP.D..DFYY.G..FG.S.PE
Retrocopy LVCANVDMKFSDDVGVEILSSLFSILHPGFHGLTRKYFEYEHQLPSQAHIPEDKEDFYYIGALFGESMPE

Parental  VYRLTTACHQAMTADQAQGIEAVWHDESHLNRYLLSHKPSKVLSPEYLWDEQML
          VYRL..ACH.AM..DQA..IEA...DESHLN.YLL.HKP.KVLSPEY.WD.Q.L
Retrocopy VYRLAKACHEAMMVDQANHIEAT*NDESHLNKYLLYHKPTKVLSPEYMWDSQIL

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	0.22 RPM
ERP005899_muscle	0.00 RPM	33.26 RPM
SRP017611_brain	0.05 RPM	0.18 RPM
SRP017611_kidney	0.00 RPM	29.04 RPM
SRP017611_liver	0.00 RPM	0.68 RPM
SRP030211_testis	3.97 RPM	0.51 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_699 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_699 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_699 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001005	1 retrocopy	retro_amel_1927,
Bos taurus	ENSBTAG00000012525	1 retrocopy	retro_btau_699 ,
Loxodonta africana	ENSLAFG00000010293	1 retrocopy	retro_lafr_1256,
Mustela putorius furo	ENSMPUG00000012419	1 retrocopy	retro_mputfur_1076,