RetrogeneDB ID: retro_btau_655

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:21513530..21513959(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000023895
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BMK
• Ensembl ID: ENSBTAG00000007740
• Aliases: None
• Description: midkine precursor [Source:RefSeq peptide;Acc:NP_776360]

Sequence

>retro_btau_655
ATGCAGCGCGGAAGCTTCCTCCTCCTCGCCCTCCTCGCCTTGCTGGTGCTCACCTCCGCGGTGGCCAAAAAGAAAGACAA
AGTGAAGAAGGGAGGCCCAGGGAGCGAGTGTGCCGAGTGGACCTGGGGTCCCTGCACCCCCAGCAGCAAGGACTGCGGCG
TGGGATTCCGCGAGGGCACCTGTGGGGCCCAGACGCAGCGCATCCGGTGCCGGGTGCCCTGTAACTGGAAGAAGGAGTTT
GGAGCTGACTGCAAGTACAAATTTGAGATCTGGGGGGCGTGTGATGGGGGCACAGGCACCAAAGCCTGCCAAGGGACCCT
GAAGAAGGCGCGATACAATGCCCAGTGCCAGGAGACCATCCGAGTGACCAAGTCCTGCAGCCCCAAGACCAAAGCCAAGG
CCAAAGCTAAGAAAGGGAAGGAAAAGGAC

Alignment

ORF - retro_btau_655 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQRRSFLLLALLALLALTSAVAKKKDKMKKGGPGSECAEWTWGPCTPSSKDCGVGFREGTCGAQTQRIRC
          MQR.SFLLLALLALL.LTSAVAKKKDK.KKGGPGSECAEWTWGPCTPSSKDCGVGFREGTCGAQTQRIRC
Retrocopy MQRGSFLLLALLALLVLTSAVAKKKDKVKKGGPGSECAEWTWGPCTPSSKDCGVGFREGTCGAQTQRIRC

Parental  RVPCNWKKEFGADCKYKFETWGACDGGTGTKARQGTLKKARYNAQCQETIRVTKPCSPKTKAKAKAKKGK
          RVPCNWKKEFGADCKYKFE.WGACDGGTGTKA.QGTLKKARYNAQCQETIRVTK.CSPKTKAKAKAKKGK
Retrocopy RVPCNWKKEFGADCKYKFEIWGACDGGTGTKACQGTLKKARYNAQCQETIRVTKSCSPKTKAKAKAKKGK

Parental  EKD
          EKD
Retrocopy EKD

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	0.72 RPM
ERP005899_muscle	0.00 RPM	14.09 RPM
SRP017611_brain	0.00 RPM	3.38 RPM
SRP017611_kidney	0.00 RPM	2.25 RPM
SRP017611_liver	0.00 RPM	0.30 RPM
SRP030211_testis	0.30 RPM	3.13 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_655 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_655 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007740	1 retrocopy	retro_btau_655 ,
Echinops telfairi	ENSETEG00000016707	2 retrocopies	retro_etel_1929, retro_etel_947,
Loxodonta africana	ENSLAFG00000015119	1 retrocopy	retro_lafr_194,
Macaca mulatta	ENSMMUG00000021448	2 retrocopies	retro_mmul_1486, retro_mmul_466,