RetrogeneDB ID: retro_btau_1700

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:42491544..42492230(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OIP5
• Ensembl ID: ENSBTAG00000010766
• Aliases: None
• Description: protein Mis18-beta [Source:RefSeq peptide;Acc:NP_001192621]

Sequence

>retro_btau_1700
ATGGCAGCTCAGCCTCAGAGGCATTGCTCTCACTTTGCAAAGCAGCTGTGGGGTGACTTTTGTGATGGGGATAAGAAGGC
GATTGATGAACCTTCTTTTACAACTTCCATGGAGTGAGACATGCAAGTGGTGAAAGGGTCTTCTCTGCTCAGCCCTGCAG
GGCTGGAGCTGGAGGAGATGCCATCCAGCCCATGACTGCTGTGGTGGTTGCAACCAGAGAGGTGCTCCATGTTCCAGTAT
GCACAGCACCGTGCTGTGCTCACTGACTCTGTGCACCTCCCCTGGGACCTGTTGAGAGCCCCTGGGGCCAGGAGCTTCTC
CAGAGTCACAATAATGTAGTTTAGGAGGCTCCCTTCCTCGTTGGCCTTGAAAGTTCCCTCAAAGGCAACACTTAAAACCT
TTTACTCTGTAGTTCCTGTGATTTTTCCATTGGTTTCCATCTGTATTCTACCTATGCTGCCCTGGCTGCCTTGAGAGGTC
ACTTCTGCCTTTCCAGTGACAAAATGGTGTGTTTCTTCTTAAAAGCAAAAGCCATAGTAGATGCACCCGAGATGGATATT
CACAACACATCTCTACCAGAAATGGTTGCAGATCTGAAAGAGAAGATGATGTTAGTGCATACTCATTTAAATTTGCTCTT
GAAGATTCTAAAGGAAGTGATTCTTGATCAGTTCAAGGCAAAAGAC

Alignment

ORF - retro_btau_1700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 93.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAARPRRHISGIAKQPQGDFCDGAKKAIDEPSFATSMEWDTQVVKGSSPVGPAGLGLEKLPSRPRLPQWL
          MAA.P.RH.S..AKQ..GDFCDG.KKAIDEPSF.TSME.D.QVVKGSS...PAGL.LE..PS.P.L..WL
Retrocopy MAAQPQRHCSHFAKQLWGDFCDGDKKAIDEPSFTTSME*DMQVVKGSSLLSPAGLELEEMPSSP*LLWWL

Parental  QPERCAVFQCAQCHAVLADSVHLAWDLSRSLGAVVFSRVT-NNVVLEAPFLVGIEGSLKGSTYNLLFCSF
          QPERC..FQ.AQ..AVL.DSVHL.WDL.R..GA..FSRVT.NNVV.EAPFLVG.E.SLKG.T.NLL.CS.
Retrocopy QPERCSMFQYAQHRAVLTDSVHLPWDLLRAPGARSFSRVT<NNVV*EAPFLVGLESSLKGNT*NLLLCSS

Parental  CEIPIGFHLYSTHAALAALRGHFCLSSDKMVCYLLKTKAIVNASEMDIHIIPLPEKVAELKEKIMLTHTR
          C...IGFHLYST.AALAALRGHFCLSSDKMVC..LK.KAIV.A.EMDIH...LPE.VA.LKEK.ML.HT.
Retrocopy CDFSIGFHLYSTYAALAALRGHFCLSSDKMVCFFLKAKAIVDAPEMDIHNTSLPEMVADLKEKMMLVHTH

Parental  LNSLMKILKEMPPDQSKKRN
          LN.L.KILKE...DQ.K...
Retrocopy LNLLLKILKEVILDQFKAKD

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	0.43 RPM
ERP005899_muscle	0.00 RPM	1.90 RPM
SRP017611_brain	0.00 RPM	0.91 RPM
SRP017611_kidney	0.00 RPM	1.36 RPM
SRP017611_liver	0.00 RPM	0.08 RPM
SRP030211_testis	1.46 RPM	3.43 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1700 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1700 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1700 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016777	1 retrocopy	retro_amel_242,
Bos taurus	ENSBTAG00000010766	1 retrocopy	retro_btau_1700 ,
Felis catus	ENSFCAG00000030520	1 retrocopy	retro_fcat_1387,
Myotis lucifugus	ENSMLUG00000009765	2 retrocopies	retro_mluc_2106, retro_mluc_2341,
Mustela putorius furo	ENSMPUG00000008828	2 retrocopies	retro_mputfur_1518, retro_mputfur_1534,
Otolemur garnettii	ENSOGAG00000033746	1 retrocopy	retro_ogar_1761,
Sorex araneus	ENSSARG00000009593	2 retrocopies	retro_sara_351, retro_sara_629,