RetrogeneDB ID: retro_cfam_1456

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:118742..119188(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL22
• Ensembl ID: ENSCAFG00000017605
• Aliases: None
• Description: mitochondrial ribosomal protein L22 [Source:HGNC Symbol;Acc:14480]

Sequence

>retro_cfam_1456
GTTTTACCCCAGTCATATATCCACATGCATAGGTCTCTGAACATTTCTCGAAAATGGGAAAAGAAGAATAAAACTGTTTA
TCCTCCACAATTACCTGGAGAACCTCGGAGACCAACAGAAATCTACCATTGTTGAAGGCAAATAAAATGCAGCAAAGACA
ATATGTGGTGTTTGGCAAAATTGGTAAAAGAATGTTCATTGACCAGGCTTTGGCTCAACTGGAATTCAGTGACAAAAAGG
GGGCCCAAATAATTAAAGAGATTCTCTTAGAAGCACAAGATATGGCAGTGAGAGATCACAATGTGGAATTCAGATCCAAT
TTATATATAACTGAGTCGACTTCAAGGCGAGGCTAATACTTGAATTCCATCCGATACCATGGCAGAGGACGCTTTGGGAT
TATGGAGATGGTTTATTGCCATTATTTTGTGAAGTTGGTAGAAGGC

Alignment

ORF - retro_cfam_1456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86. %
• Parental protein coverage: 82.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLPQSYIHTSGSLDISRKWEKKNKIVYPPQLPGEPRRPAEIYHCRRQIKYSKDKMWYLAKLIRGMS-IDQ
          VLPQSYIH...SL.ISRKWEKKNK.VYPPQLPGEPRRP.EIYHC.RQIK.SKD.MW.LAKL....S.IDQ
Retrocopy VLPQSYIHMHRSLNISRKWEKKNKTVYPPQLPGEPRRPTEIYHC*RQIKCSKDNMWCLAKLVKECS<IDQ

Parental  ALAQLEFSDKKGAQIIKEILLEAQDMAVRDHNVEFRSNLYIAESTSGRGQYLKRIRYHGRGRFGIMEKVY
          ALAQLEFSDKKGAQIIKEILLEAQDMAVRDHNVEFRSNLYI.ESTS.RG.YL..IRYHGRGRFGIME.VY
Retrocopy ALAQLEFSDKKGAQIIKEILLEAQDMAVRDHNVEFRSNLYITESTSRRG*YLNSIRYHGRGRFGIMEMVY

Parental  CHYFVKLVEG
          CHYFVKLVEG
Retrocopy CHYFVKLVEG

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	0.04 RPM	17.85 RPM
SRP017611_brain	0.00 RPM	7.78 RPM
SRP017611_kidney	0.00 RPM	30.05 RPM
SRP017611_liver	0.00 RPM	4.64 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1456 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1456 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1456 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003875	1 retrocopy	retro_acar_88,
Bos taurus	ENSBTAG00000019457	1 retrocopy	retro_btau_1348,
Canis familiaris	ENSCAFG00000017605	2 retrocopies	retro_cfam_1456 , retro_cfam_584,
Macaca mulatta	ENSMMUG00000021229	1 retrocopy	retro_mmul_1889,
Otolemur garnettii	ENSOGAG00000016777	1 retrocopy	retro_ogar_1042,
Vicugna pacos	ENSVPAG00000001170	1 retrocopy	retro_vpac_294,