RetrogeneDB ID: retro_btau_324

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:4842898..4843788(+)
• Located in intron of: ENSBTAG00000016644

Retrocopy information

• Ensembl ID: ENSBTAG00000035005
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL15
• Ensembl ID: ENSBTAG00000001174
• Aliases: None
• Description: 39S ribosomal protein L15, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q0VC21]

Sequence

>retro_btau_324
ATGGTTGGCCCGGTGCGGGGCGCAGCAGGGCCTTGGGCCCTGGACCTGCTTTGGGCCCTGCCTCGTGTGAGCCTGGCTAA
CCTGAGGCCGAACCCGGGCTCCAGGAAACCGCAAAGACGACGAAGAGGTCAGAGAAGAGGTAGGAAGTGTGGCAGGGGCC
ACAAAAGAGAATGGCAGAGAGGAACCCGGCCCCGGCTGGGCTTTGAAGGAGGCCAGACTCCATTTTACCTTCAAATCCCA
AAATACGGCTTTAATGAAGGACACAGCTTCAGACGCCAGTATCAGCCTTTGAGTCTCAACAGGCTGCAGTACCTGATTGA
CCTGGGCCGTGTCGATCCCACACAACCTATTGACTTAACCCAGCTGGTCAACGGGCGAGGTGTTACCATCCAGCCATCTA
AAAGGGACTATGGAGTGCAGTTGGTAGAGGAGGGCGCTGACACCTTTAAGGCAAAAGTTAACATCGAAGTTCAGCTGGCT
TCTGAGCTGGCCATCGCCGCCATCGAGAAGAACGGGGGTGTCGTCACGACCGCCTTCTATGACCCGCGAAGCCTGGAAAT
TCTGTGCAAACCCATCCCATTCTTTCTCCGTGGACAACCCATTCCCAAGCGGATGCTCCCCCCCGAGGCCTAGTCCCCTA
CTACACTGACGCGAGAAATCGAGGCTATCTGGCGAATCCTGCCAGATTTCCCGAAACGAGACTGGAGCTCGCCAAGAAGT
ATGGCTATATTTTACCCGACATCACTAAAGACGAACTCTTCAAAATGCTCAGTTCTCGGAAGGATCCACGGCAGATTTTC
TTTGGTCTGGCTCCCGGATGGGTGGTGAACATGGCAGACAAGAAGATTCTGAAACCTACGGATGAGAAGCTGCTTGAGTA
CTACAGCTCC

Alignment

ORF - retro_btau_324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.98 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGPVRGAAGPWALDLLRALPRVSLANLRPNPGSRKPERRRRGQRRGRKCGRGHKGERQRGTRPRLGFEG
          M.GPVRGAAGPWALDLL.ALPRVSLANLRPNPGSRKP.RRRRGQRRGRKCGRGHK.E.QRGTRPRLGFEG
Retrocopy MVGPVRGAAGPWALDLLWALPRVSLANLRPNPGSRKPQRRRRGQRRGRKCGRGHKREWQRGTRPRLGFEG

Parental  GQTPFYLRIPKYGFNEGHSFRRQYQPLSLNRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPSKRDYGVQ
          GQTPFYL.IPKYGFNEGHSFRRQYQPLSLNRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPSKRDYGVQ
Retrocopy GQTPFYLQIPKYGFNEGHSFRRQYQPLSLNRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPSKRDYGVQ

Parental  LVEEGADTFKAKVNIEVQLASELAIAAIEKNGGVVTTAFYDPRSLEILCKPIPFFLRGQPIPKRMLPPEA
          LVEEGADTFKAKVNIEVQLASELAIAAIEKNGGVVTTAFYDPRSLEILCKPIPFFLRGQPIPKRMLPPEA
Retrocopy LVEEGADTFKAKVNIEVQLASELAIAAIEKNGGVVTTAFYDPRSLEILCKPIPFFLRGQPIPKRMLPPEA

Parental  -LVPYYTDARNRGYLADPARFPEARLELAKKYGYILPDITKDELFKMLSSRKDPRQIFFGLAPGWVVNMA
          .LVPYYTDARNRGYLA.PARFPE.RLELAKKYGYILPDITKDELFKMLSSRKDPRQIFFGLAPGWVVNMA
Retrocopy <LVPYYTDARNRGYLANPARFPETRLELAKKYGYILPDITKDELFKMLSSRKDPRQIFFGLAPGWVVNMA

Parental  DKKILKPTDEKLLEYYSS
          DKKILKPTDEKLLEYYSS
Retrocopy DKKILKPTDEKLLEYYSS

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	18.24 RPM
ERP005899_muscle	0.05 RPM	25.02 RPM
SRP017611_brain	0.14 RPM	22.06 RPM
SRP017611_kidney	0.00 RPM	21.04 RPM
SRP017611_liver	0.15 RPM	23.71 RPM
SRP030211_testis	19.71 RPM	36.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_324 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_324 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001174	1 retrocopy	retro_btau_324 ,
Canis familiaris	ENSCAFG00000006988	2 retrocopies	retro_cfam_1573, retro_cfam_511,
Choloepus hoffmanni	ENSCHOG00000005299	3 retrocopies	retro_chof_1379, retro_chof_1719, retro_chof_746,
Callithrix jacchus	ENSCJAG00000016719	1 retrocopy	retro_cjac_2230,
Dasypus novemcinctus	ENSDNOG00000017664	1 retrocopy	retro_dnov_364,
Erinaceus europaeus	ENSEEUG00000001454	2 retrocopies	retro_eeur_128, retro_eeur_707,
Echinops telfairi	ENSETEG00000001724	1 retrocopy	retro_etel_1304,
Mustela putorius furo	ENSMPUG00000010533	1 retrocopy	retro_mputfur_149,
Mus musculus	ENSMUSG00000033845	2 retrocopies	retro_mmus_1709, retro_mmus_3534,
Ornithorhynchus anatinus	ENSOANG00000007286	1 retrocopy	retro_oana_114,
Otolemur garnettii	ENSOGAG00000003768	1 retrocopy	retro_ogar_534,
Ochotona princeps	ENSOPRG00000000921	2 retrocopies	retro_opri_241, retro_opri_364,
Rattus norvegicus	ENSRNOG00000008566	2 retrocopies	retro_rnor_1344, retro_rnor_2785,
Sus scrofa	ENSSSCG00000030578	1 retrocopy	retro_sscr_617,
Tarsius syrichta	ENSTSYG00000014106	1 retrocopy	retro_tsyr_37,
Tursiops truncatus	ENSTTRG00000011844	2 retrocopies	retro_ttru_1139, retro_ttru_733,