RetrogeneDB ID: retro_btau_329

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:8139929..8140247(+)
• Located in intron of: ENSBTAG00000034823

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL23
• Ensembl ID: ENSBTAG00000000103
• Aliases: None
• Description: 39S ribosomal protein L23, mitochondrial [Source:RefSeq peptide;Acc:NP_001071352]

Sequence

>retro_btau_329
ATGACCAGAGTGGACCTCAGGAACTACCTCGAGCGCGTCTACAATGTGCCGGTGGCCGCCGTGCGGACGAGGGTGCAGCA
CGGTTCCAACAGGAGGAGGGATCACAGGAACGTCAGGATAAAGCAGCCAGACTATAAGGTGGCCTACGTGCAGCTGGCAC
ACGGGCAGACCTTCACATTCCCAGATCTGTTTCCCAAGGGGAAGCGGCCCGGCGGCAGCTCCGCGGACGAGGACCTCCGG
GTCCAGGTGCTGGAGGAGCAGCAGCAACGTCAGAGCCCCGACCCGCGGCGCGGGGGCGTCCCCAGCTGGTTTGGCCTG

Alignment

ORF - retro_btau_329 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTRVDLRNYLERVYNVPVAAVRTRVQHGSNRRRDHRNVRIKQPDYKVAYVQLAHGQTFTFPDLFPKGKRP
          MTRVDLRNYLERVYNVPVAAVRTRVQHGSNRRRDHRNVRIKQPDYKVAYVQLAHGQTFTFPDLFPKGKRP
Retrocopy MTRVDLRNYLERVYNVPVAAVRTRVQHGSNRRRDHRNVRIKQPDYKVAYVQLAHGQTFTFPDLFPKGKRP

Parental  GGSSADEDLRDQVLEEQQQRQSPDPRRGGVPSWFGL
          GGSSADEDLR.QVLEEQQQRQSPDPRRGGVPSWFGL
Retrocopy GGSSADEDLRVQVLEEQQQRQSPDPRRGGVPSWFGL

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	18.31 RPM	42.18 RPM
ERP005899_muscle	1.37 RPM	28.88 RPM
SRP017611_brain	0.82 RPM	2.83 RPM
SRP017611_kidney	3.44 RPM	50.91 RPM
SRP017611_liver	4.98 RPM	48.02 RPM
SRP030211_testis	1.75 RPM	10.32 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_329 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_329 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	ENSBTAG00000000103	1 retrocopy	retro_btau_329 ,
Macaca mulatta	ENSMMUG00000031268	1 retrocopy	retro_mmul_1226,
Mus musculus	ENSMUSG00000037772	1 retrocopy	retro_mmus_2046,
Nomascus leucogenys	ENSNLEG00000026950	1 retrocopy	retro_nleu_1043,
Otolemur garnettii	ENSOGAG00000029988	1 retrocopy	retro_ogar_372,
Sarcophilus harrisii	ENSSHAG00000002716	1 retrocopy	retro_shar_411,