RetrogeneDB ID: retro_cfam_511

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:20553036..20553912(-)
• Located in intron of: ENSCAFG00000002264

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL15
• Ensembl ID: ENSCAFG00000006988
• Aliases: None
• Description: mitochondrial ribosomal protein L15 [Source:HGNC Symbol;Acc:14054]

Sequence

>retro_cfam_511
GTGCAGGCCGGCGGGGCAAGAACCCTGGACCTGCTCCGGGCCTTGCCCCGTGTGAGCTTGGCCAACCTAAAACCAAATCC
AGGCTCCAGGAAACCGGAAAGACGGCGAAGAGGTCAGAGAAGAGGTAGAAAATGTGGCCGAGGCCATAAAGGAGAGCGGC
AGAGAGGAACCCGGCCCAGACTGGGTTTTGAGGGAGGCCAAACCCCATTTTACATTTGAATCCCAAAATACAGGTTTAAT
GAAGGTCATAGCTTCAGACGCCAGTATCAGCCTTTGAGTCTCAATAGATTGCAATATCTTATTGATTTGGGTCGCGTGGA
TCCTACTCAACCTATTGACCTAACTCAACTTGTCAATGGGAGAGGTGTGACCATCCAGCCACTTAAAAGGGATTATGGTG
TCCAGCTGGTAGAGGAGGGTGCTGACACCTTTAAGGCGAAAGTTAATATTGAAGTACAGTTGGCTTCAGAATTAGCCATT
GCTGCAATTGAAAAAAATGGTGGTGTTGTTACTACAGCTTTTTATGATCCAAGAAGTCTAGAAATTCTGTGCAAACCTGT
TCCATTCTTTCTGCGTGGACAACCTATTCCAAAACGAATGCTTCCTCCTGAAGCACTGGTACCGTATTATACCGATGCAA
AGAATCGTGGTTACCTGGCGGATCCTGCCAAATTTCCTGAAGCAAGACTTGAACTTGCCAAGAAGTACGGCTATATTTTA
CCTGATATCGCTAAAGACGAGCTCTTCAAAATGCTTAGTACTCGAAAGGATCCAAGGCAGATTTTCTTTGGTCTTGCCCC
TGGATGGGTGGTGAATATGACAGATAAGAAAATCCTAAAACCTACAGATGAGAATCTCCTCAAGTATTATAGCTCA

Alignment

ORF - retro_cfam_511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQAGGARTLDLLRALPRVSLANLKPNPGSRKPERRRRGRRRGRKCGRGHKGERQRGTRPRLGFEGGQTPF
          VQAGGARTLDLLRALPRVSLANLKPNPGSRKPERRRRG.RRGRKCGRGHKGERQRGTRPRLGFEGGQTPF
Retrocopy VQAGGARTLDLLRALPRVSLANLKPNPGSRKPERRRRGQRRGRKCGRGHKGERQRGTRPRLGFEGGQTPF

Parental  YIRIPKYGFNEGHSFRRQYQPLSLNRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPLKRDYGVQLVEEG
          YI.IPKY.FNEGHSFRRQYQPLSLNRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPLKRDYGVQLVEEG
Retrocopy YI*IPKYRFNEGHSFRRQYQPLSLNRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPLKRDYGVQLVEEG

Parental  ADTFKAKVNIEVQLASELAIAAIEKNGGVVTTAFYDPRSLEILCKPVPFFLRGQPIPKRMLPPEALVPYY
          ADTFKAKVNIEVQLASELAIAAIEKNGGVVTTAFYDPRSLEILCKPVPFFLRGQPIPKRMLPPEALVPYY
Retrocopy ADTFKAKVNIEVQLASELAIAAIEKNGGVVTTAFYDPRSLEILCKPVPFFLRGQPIPKRMLPPEALVPYY

Parental  TDAKNRGYLADPAKFPEARLELAKKYGYILPDITKDELFKMLSTRKDPRQIFFGLAPGWVVNMTDKKILK
          TDAKNRGYLADPAKFPEARLELAKKYGYILPDI.KDELFKMLSTRKDPRQIFFGLAPGWVVNMTDKKILK
Retrocopy TDAKNRGYLADPAKFPEARLELAKKYGYILPDIAKDELFKMLSTRKDPRQIFFGLAPGWVVNMTDKKILK

Parental  PTDENLLKYYSS
          PTDENLLKYYSS
Retrocopy PTDENLLKYYSS

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
SRP012049_cerebellum	0.00 RPM	16.84 RPM
SRP017611_brain	0.56 RPM	13.18 RPM
SRP017611_kidney	0.66 RPM	35.66 RPM
SRP017611_liver	0.44 RPM	10.37 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_511 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_511 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,