RetrogeneDB ID: retro_btau_1165

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:36934515..36934988(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.49010
• Ensembl ID: ENSBTAG00000001212
• Aliases: None
• Description: translocon-associated protein subunit beta precursor [Source:RefSeq peptide;Acc:NP_001015533]

Sequence

>retro_btau_1165
TTAGATGTGGAATTATCTGATGACTTTTTCCCTCTAGAAGTTTTCTTTGACATTGTCTCTGGGATGCGCAGTGTCAAATG
GGATCAGATTGCATCTGCTAGCAGCATCTCCCACATGGTCCTGCACCCTCTCAAGGCTGGTTATTTCACTTCACCTCAGC
AACTACTACTTGCTTGGCCCAGGAGGATGGGTCCCTTGTGATGGGCTTTTCCAGTGCAACTGGACAGGAAAGATCCCTGG
CTCAGTGGGAGTTTGATAGGGGATTCTCCCTCCATTTCCTGGACTGGATGACCTTTGGGGTCATGACTCTCCCTCCCATT
GACATACCCCTGCAGTTGTGGAACTCCAGCAAGAGGAAATATGACACCCCCAAAGTCAAGAAAAAGTGAATGGGGTCTTC
CACAGCCCTTCCTTCCCAAGATGTCCAGGTGCTTTCCAGACTCCAAAGGGTATCTCAAATGCAATCTCTTCTC

Alignment

ORF - retro_btau_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.62 %
• Parental protein coverage: 74.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDVELSDDSFPPEDF-GIVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYF-NFTSATVTYLAQEDGPVVI
          LDVELSDD.FP.E.F..IVSGM..VKWD.IA.AS..SH..VL.PLKAGYF..FTSAT.T.LAQEDG..V.
Retrocopy LDVELSDDFFPLEVFFDIVSGMRSVKWDQIASASSISH-MVLHPLKAGYF<HFTSATTTCLAQEDGSLVM

Parental  GFTSAPGQGGILAQREFDRRFSPHFLDWAAFGVMTLPSIGVPLLLWYSSKRKYDTPKTKRL-SGASTALP
          GF.SA.GQ...LAQ.EFDR.FS.HFLDW..FGVMTLP.I..PL.LW.SSKRKYDTPK.K....G.STALP
Retrocopy GFSSATGQERSLAQWEFDRGFSLHFLDWMTFGVMTLPPIDIPLQLWNSSKRKYDTPKVKKK*MGSSTALP

Parental  AQEIQVLSRLQRESQMQCLL
          .Q..QVLSRLQR.SQMQ.LL
Retrocopy SQDVQVLSRLQRVSQMQSLL

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	0.07 RPM	85.87 RPM
ERP005899_muscle	0.00 RPM	336.37 RPM
SRP017611_brain	0.00 RPM	66.28 RPM
SRP017611_kidney	0.00 RPM	112.44 RPM
SRP017611_liver	0.00 RPM	219.20 RPM
SRP030211_testis	0.00 RPM	55.10 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1165 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1165 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001212	2 retrocopies	retro_btau_1165 , retro_btau_675,
Cavia porcellus	ENSCPOG00000023729	1 retrocopy	retro_cpor_478,
Nomascus leucogenys	ENSNLEG00000012304	1 retrocopy	retro_nleu_3102,
Ictidomys tridecemlineatus	ENSSTOG00000028971	1 retrocopy	retro_itri_1381,