RetrogeneDB ID: retro_btau_975

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:41450818..41451608(+)
• Located in intron of: ENSBTAG00000014418

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSBTAG00000047236
• Aliases: None
• Description: None

Sequence

>retro_btau_975
CAGGACCAGAAAAGTCCCTTGCCCAAGACCATTCCTGAAAGAGGTTAAATGGAGGGTATGGCACCCAAGGAGAACTTGGA
GAAGGACTTGATGGGAGACATGGAAGAGATAAGAACCCATTAATCTGAAAAGCCTGGACTTCTGAAGGCTCCTGAGGGAG
AAGTTTGAACTAACAGTGGATTCAGAAGACATTCTCTTAGGAGTCACAGATGTTTCAAAAGGAAATGGACCAACAGCCCC
ACATTCCAAGAAGTGCGTCAAGAAGAAACCACATCTTTGGACAAAGAGTTCTCAGGAAAACTTGGGTCTCTTTCCATTGG
TTCACCTGGCACTGTGGGATCCACCAGTCTTCCTAATGGAAAAGAAACCTGGGGTAGGGCATCCTATGAATATAGGGTAT
GCAAGAAGAAATTTCCTTATCAATCTCAGCTTACTCTGCACCAGAGGACACATGCAGGCAAGAGCTCCTTTAAATGCAGT
ATTTGTGTCAAAGGTTCATGCAGCCTTCAAATTTTTGCGTTCACCAGTGGATCCACACAGGCAAGAAGCCATACTGCTGT
GATCTGTGCCCCAAGAAGTTCACCAGCATCTCCACACCTGCTCATGAGAGGACCCGCACCCAGGAGAAGCTTTCCAGTGT
GAGCTCTGTGACAAGCCCTTCAGCCACAGTGGGGACCGCAGTGTTCACTGACGCACCCACTCTTGGCTCAAACCCTACGT
GTGTCCCGAGTGTCACAGTACCTTCCATCGGCTGGCGACTTTCGTATATCACCAGGAAAGCCATTCTAAA

Alignment

ORF - retro_btau_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.36 %
• Parental protein coverage: 70.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QHQKALLPETIPETGQLEGQTPSKEYLVKDVLEDTGVTRTLSSQEPELLQDREGDVSTPSGSRGGPLKNR
          Q.QK..LP.TIPE.G..EG..P.KE.L.KD...D....RT..S..P.LL...EG.V.T.SG.R...L...
Retrocopy QDQKSPLPKTIPERG*MEGMAP-KENLEKDLMGDMEEIRTH*SEKPGLLKAPEGEV*TNSGFRRHSLRSH

Parental  RRVKRKRDSSPTCQDVCQEAATCLDQEEFSGQLGSRSVGASGTVGPTSLPERAETLGRAPSECKVCKKSF
          R..KRK...SPT.Q.V.QE..T.LD.E.FSG.LGS.S.G..GTVG.TSLP...ET.GRA..E..VCKK.F
Retrocopy RCFKRKWTNSPTFQEVRQEETTSLDKE-FSGKLGSLSIGSPGTVGSTSLPNGKETWGRASYEYRVCKKKF

Parental  PYQSQLTVHQRTHTGERPFQCDICAKG-FIQLSDLRVHEQIHTGVKPYSCDLCLKKFTHDSTLHTHKRTH
          PYQSQLT.HQRTH.G...F.C.IC.KG.F.Q.S...VH..IHTG.KPY.CDLC.KKFT..ST...H.RT.
Retrocopy PYQSQLTLHQRTHAGKSSFKCSICVKG<FMQPSNFCVHQWIHTGKKPYCCDLCPKKFTSIST-PAHERTR

Parental  TQEK-PFRCEHCDRAFSHRGNLNVHRRTHSGLKPYVCPECHSAFRQLGTFTHHQKIHSR
          TQEK..F.CE.CD..FSH.G...VH.RTHS.LKPYVCPECHS.F..L.TF..HQ..HS.
Retrocopy TQEK<AFQCELCDKPFSHSGDRSVH*RTHSWLKPYVCPECHSTFHRLATFVYHQESHSK

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	0.00 RPM
ERP005899_muscle	0.11 RPM	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.02 RPM	1.50 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_975 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_975 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_975 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047236	1 retrocopy	retro_btau_975 ,
Myotis lucifugus	ENSMLUG00000012011	1 retrocopy	retro_mluc_30,
Mus musculus	ENSMUSG00000058028	3 retrocopies	retro_mmus_1078, retro_mmus_1953, retro_mmus_2723,