RetrogeneDB ID: retro_btau_140

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:54649605..54650250(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000022275
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL10
• Ensembl ID: ENSBTAG00000007454
• Aliases: RPL10, QM
• Description: 60S ribosomal protein L10 [Source:UniProtKB/Swiss-Prot;Acc:Q9XSI3]

Sequence

>retro_btau_140
ATGGGCCGCCGCCCTGCCCGGTGTTACCGGTATTGTAAGAACAAGCCGTACCCAAAGTCTCGCTTCTGCCGAGGTGTCCC
TGATGCTAAGATTCGCATCTTCGACTTGGGGCGTAAGAAGGCCAAAGTGGATGAGTTCCCACTCTGTGGCCACATGGTGT
CAGATGAGTATGAGCAGCTCTCCTCTGAAGCCCTGGAGGCTGCCCGTATTTGTGCCAACAAGTACATGGTGAAAAGTTGT
GGCAAAGATGGTTTTCACATCCGAGTGCGGCTCCACCCCTTCCATGTCATCCGTATCAACAAGATGTTGTCTTGCGCTGG
AGCTGATAGACTCCAGACAGGTATGCGCGGTGCCTTTGGAAAGCCCCAGGGCACAGTGGCCAGGGTCCACAGTGGCCAGG
TCATAATGTCCATCCGCACCAAGCTGCAGAACAAGGAACATGTGATTGAAGCCCTCCGCCGGGCCAAGTTCAAGTTCCCT
GGCCGCCAGAAGATCCACATCTCTAAGAAGTGGGGATTTACCAAGTTCAACGCGGATGAATTTGAGAACATGGTGGCAGA
AAAGCGACTCATCCCAGACGGCTGTGGGGTCAAATACATCCCTAATCGTGGTCCTCTGGACAAATGGCGGGCCCTGCACT
CATGA

Alignment

ORF - retro_btau_140 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
          MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
Retrocopy MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
          CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVH.GQVIMSIRT
Retrocopy CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHSGQVIMSIRT

Parental  KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFENMVAEKRLIPDGCGVKYIPNRGPLDKWR
          KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFENMVAEKRLIPDGCGVKYIPNRGPLDKWR
Retrocopy KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFENMVAEKRLIPDGCGVKYIPNRGPLDKWR

Parental  ALHS
          ALHS
Retrocopy ALHS

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	289.03 RPM
ERP005899_muscle	3.33 RPM	1811.83 RPM
SRP017611_brain	0.09 RPM	123.06 RPM
SRP017611_kidney	0.36 RPM	446.49 RPM
SRP017611_liver	0.23 RPM	359.27 RPM
SRP030211_testis	0.09 RPM	36.62 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_140 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_140 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007454	2 retrocopies	retro_btau_140 , retro_btau_99,
Cavia porcellus	ENSCPOG00000002355	1 retrocopy	retro_cpor_64,
Equus caballus	ENSECAG00000017154	1 retrocopy	retro_ecab_113,
Homo sapiens	ENSG00000147403	3 retrocopies	retro_hsap_2030, retro_hsap_3265, retro_hsap_3437,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Microcebus murinus	ENSMICG00000004658	2 retrocopies	retro_mmur_1077, retro_mmur_4,
Myotis lucifugus	ENSMLUG00000014337	3 retrocopies	retro_mluc_1592, retro_mluc_191, retro_mluc_275,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Mustela putorius furo	ENSMPUG00000009320	3 retrocopies	retro_mputfur_1405, retro_mputfur_54, retro_mputfur_84,
Mus musculus	ENSMUSG00000008682	1 retrocopy	retro_mmus_71,
Otolemur garnettii	ENSOGAG00000000099	3 retrocopies	retro_ogar_293, retro_ogar_2995, retro_ogar_3284,
Pongo abelii	ENSPPYG00000020874	5 retrocopies	retro_pabe_173, retro_pabe_1854, retro_pabe_2036, retro_pabe_2843, retro_pabe_2955,
Ictidomys tridecemlineatus	ENSSTOG00000011857	2 retrocopies	retro_itri_174, retro_itri_506,