RetrogeneDB ID: retro_btau_702

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:47904702..47905503(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR61
• Ensembl ID: ENSBTAG00000015944
• Aliases: None
• Description: WD repeat-containing protein 61 [Source:UniProtKB/Swiss-Prot;Acc:Q32LN7]

Sequence

>retro_btau_702
ATGACCAACCAGTACAGTGCTCTCTTCAGACAAGAGCACACCCATGATGATGCCATCTGATCAGTTGCCTGAGGGTCAAA
CAAAGAAGACTCTGAGACAGTGGTCATAGGATCCCTGGATGACCAAGAGAAGGTCTGGAAATGGCGTGATGAGAAACTGG
ACCTACAGTGGAATCTGGAGAGCCCTCAGCTGAGTGTGTTGTTTGTGGACTTCAGCCACACCCTACCCATGGCTGCATCC
CATTCTGTTGATGCTCATATTCTCCTCTGGCAGTTGGAAAAGAGCAAATAAAGAAAGTCTGTAGATGCAGGACCTGTGGA
TGCATGGACTTTGGCCTTTTCTCCCGATTCCCAGAATCTGTCCACAAGAACTCATGTGGGGAAAGTGAACATTTTTGATG
TGGAAAGTGGGAAAAATGAGTATTCTTTGGACATAAGAGGAAAATTCATTCTTAGTATTGCATATTGTCCTGATGGGAAG
TTTCTGGCCAGTAGAGCCATAGGTGGAATCATCAGTATTTTTGATATCACAACTGGGAATCTTCTGCATATACTAGAAGG
TCATGATATGCCCATTCGCTCCTTGACTTTTTCCCTGGAGTCACAGATCCTTGTAATTGCTTTGGATGATGGCTCCATCA
AGATCTGTGACGTACAACACGCCAGCTTGGCTGGCACATTGGGTGTCCCTGCATCCTGGGTGCTGAACGTTGCATTTTGT
CCTGGTGACACACACTTGGTTTCCAGTTGATCTGACAAAAGTGTAAAAGTGGGATGTTGGAATGAGGACTTGTGTTCACA
C

Alignment

ORF - retro_btau_702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.75 %
• Parental protein coverage: 87.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTNQYSILFKQEQAHDDAIWSVAWGSNKKENSETVVTGSLDDLVKVWKWRDEKLDLQWSLEGHQLGVVSV
          MTNQYS.LF.QE..HDDAI.SVA.GSNK.E.SETVV.GSLDD..KVWKWRDEKLDLQW.LE..QL.V..V
Retrocopy MTNQYSALFRQEHTHDDAI*SVA*GSNK-EDSETVVIGSLDDQEKVWKWRDEKLDLQWNLESPQLSVLFV

Parental  DISHTLPIAASSSLDAHIRLWDLENGKQIKSIDAGPVDAWTLAFSPDSQYLATGTHVGKVNIFGVESGKK
          D.SHTLP.AAS.S.DAHI.LW.LE..K..KS.DAGPVDAWTLAFSPDSQ.L.T.THVGKVNIF.VESGK.
Retrocopy DFSHTLPMAASHSVDAHILLWQLEKSK*RKSVDAGPVDAWTLAFSPDSQNLSTRTHVGKVNIFDVESGKN

Parental  EYSLDTRGKFILSIAYSPDGKYLASGAIDGIINIFDIATGKLLHTLEGHAMPIRSLTFSPDSQLLVTASD
          EYSLD.RGKFILSIAY.PDGK.LAS.AI.GII.IFDI.TG.LLH.LEGH.MPIRSLTFS..SQ.LV.A.D
Retrocopy EYSLDIRGKFILSIAYCPDGKFLASRAIGGIISIFDITTGNLLHILEGHDMPIRSLTFSLESQILVIALD

Parental  DGYIKIYDVQHANLAGTLSGHASWVLNVAFCPDDTHFVSSSSDKSVKVWDVGTRTCVH
          DG.IKI.DVQHA.LAGTL...ASWVLNVAFCP.DTH.VSS.SDKSVKV.......C.H
Retrocopy DGSIKICDVQHASLAGTLGVPASWVLNVAFCPGDTHLVSS*SDKSVKVGCWNEDLCSH

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	21.48 RPM
ERP005899_muscle	0.00 RPM	28.24 RPM
SRP017611_brain	0.00 RPM	17.50 RPM
SRP017611_kidney	0.00 RPM	31.35 RPM
SRP017611_liver	0.00 RPM	13.67 RPM
SRP030211_testis	0.03 RPM	58.13 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_702 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_702 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_702 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015944	1 retrocopy	retro_btau_702 ,
Bos taurus	ENSBTAG00000034225	1 retrocopy	retro_btau_1300,
Echinops telfairi	ENSETEG00000004321	1 retrocopy	retro_etel_1046,
Macropus eugenii	ENSMEUG00000015991	1 retrocopy	retro_meug_744,
Oryctolagus cuniculus	ENSOCUG00000009040	1 retrocopy	retro_ocun_1570,
Tupaia belangeri	ENSTBEG00000009390	1 retrocopy	retro_tbel_48,