RetrogeneDB ID: retro_cfam_51

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:20899444..20901241(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000013554
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000018145
• Aliases: None
• Description: None

Sequence

>retro_cfam_51
ATGGATGCTCACGATCTCTTTCGCCGGCTGGGCGTGGGAGCCAAATTCGATGTGAGACATTTCTCCGCGGATGCAGCGCG
ATTCCAGGTAGGAAAAAGAAAATATGACTTTGATTCTTCAGAGGTGCTGCAGGGACTCGACTTCTTTGGAAACAAGAAGT
CTGTCCCAGGTGAGTGCGGAGCATCAAGAACTCATCAGGAGCTTCAAGATGAAGAGAAAAAAGAAGAGAGCCTAACTGAA
AGGAAGAGGGAGCAGAACAAGAAAAAGAGGAAGATGATATCAGAAATTATTTCTCAAGAAGAAGGTTCTACTATACAGTG
GACATCGTCTGTGGAAGCAAAGATTGAAGATAAAAAAATTAAAAGAGAGAATAAACTAACTTCAGGAAAGTTGGAGAATC
TCAGAAAAGAAAAGATAAACTTCTTCCGGAATAAACACAAAATTCATGTCCAAGGAACTGATCTTCCTGACCCTATTGCT
ACATTTCAGCAACTTGACCAGGAATATAAAATCAATTCTCGACTGCTTCAGAACATTCTAGATGCAGGCTTCCAAACTCC
TACACCAATCCAAATGCAAGCCATTCCAGTTATGCTGCATGGTCGAGAACTTCTGGCTTCTGCTCCTACTGGATCTGGAA
AGACTTTGGCTTTTAGTATTCCCATTTTGATGCAACTAAAACAACCCACAAATAAAGGCTTCAGAGCTCTGATTATATCA
CCAACACGAGAACTTGCGAACCAGATTCACAGAGAGTTAGTAAAAATCTCTGAGGGAACAGGATTCAGGATACACATGAT
CCACAAAGCGGCAGTGGCAGCCAAGAAATTTGGACCTAAATCATCAAAGAAGTTTGATATTCTTGTGACTACTCCAAATC
GACTAATCTATTTATTAAAGCAGGATCCTCCAGGAATAGATTTAACAAGTGTTGAATGGCTGGTAGTAGATGAATCAGAC
AAACTGTTTGAAGATGGCAAAACTGGGTTCAGAGACCAGCTGGCTTCCATTTTCCTGGCCTGCACATCCCATAAGGTCAG
AAGAGCTATGTTCAGTGCAATTTTTGCATATGATGTTGAGCAGTGGTGCAAACTCAACCTGGACAATGTCATTACTGTAT
CCATTGGAGCAAGGAATTCTGCAGTAGAGACCGTAGAACAAGAGCTTCTCTTTGTTGGGTCTGAGACTGGGAAACTTCTG
GCCATGAGAGAACTTGTTAAAAAGGGTTTCAATCCCCCTGTTCTTGTTTTTGTTCAGTCCATTGAAAGGGCTAAAGAACT
TTTTCATGAGCTCATATATGAAGGTATTAATGTAGATGTTATTCATGCAGACAGAACACAGCAACAGAGAGATAACACAG
TCCACAGCTTCCGAGCTGGAAAAATCTGGGTTCTTATTTGTACAGCCTTGCTAGCCAGAGGGATTGATTTTAAAGGTGTG
AACTTGGTGATCAACTATGACTTTCCAACCAGCTCAGTGGAATATATCCACAGGATAGGTCGAACTGGAAGAGCAGGGCA
TAAAGGAAAAGCTGTTACATTTTTCACTGAAGATGATAAACCATTATTAAGAAGCGTTGCCAATGTTATACAGCAGGCTG
GATGTCCTGTGCCAGAATACATAAAAGGTTTCCAAAAACTACTAAGCAAACAAAAGAAAAAGATGATTAAGAAGCCATTG
GAAAGGGAGAGCATTAGTACAACTCCAAAATATTTCTTAGAAAAAGCTAAGAATAAACGGAAAAAGGTCACTGCTCAGAA
CAGCAAGAAGAAAGTAACTCTTGAAGACAAAAGTTAA

Alignment

ORF - retro_cfam_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDAHDLFRRLGVGAKFDVRRFSADAARFQVGKRKYDFDSSEVLQGLDFFGNKKSVPGERGASRTHQELQD
          MDAHDLFRRLGVGAKFDVR.FSADAARFQVGKRKYDFDSSEVLQGLDFFGNKKSVPGE.GASRTHQELQD
Retrocopy MDAHDLFRRLGVGAKFDVRHFSADAARFQVGKRKYDFDSSEVLQGLDFFGNKKSVPGECGASRTHQELQD

Parental  EEKKEESLTERKREQNKKKRKMISGILEIISQEEGSTIQWTSSVEAKIEDKKIKRENKLTSGKLENLRKE
          EEKKEESLTERKREQNKKKRKMIS...EIISQEEGSTIQWTSSVEAKIEDKKIKRENKLTSGKLENLRKE
Retrocopy EEKKEESLTERKREQNKKKRKMIS---EIISQEEGSTIQWTSSVEAKIEDKKIKRENKLTSGKLENLRKE

Parental  KINFFRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQTPTPIQMQAIPVMLHGRELLAS
          KINFFRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQTPTPIQMQAIPVMLHGRELLAS
Retrocopy KINFFRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQTPTPIQMQAIPVMLHGRELLAS

Parental  APTGSGKTLAFSIPILMQLKQPTNKGFRALIISPTRELANQIHRELVKISEGTGFRIHMIHKAAVAAKKF
          APTGSGKTLAFSIPILMQLKQPTNKGFRALIISPTRELANQIHRELVKISEGTGFRIHMIHKAAVAAKKF
Retrocopy APTGSGKTLAFSIPILMQLKQPTNKGFRALIISPTRELANQIHRELVKISEGTGFRIHMIHKAAVAAKKF

Parental  GPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVR
          GPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVR
Retrocopy GPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVR

Parental  RAMFSATFAYDVEQWCKLNLDNVITVSIGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFNPPVLVF
          RAMFSA.FAYDVEQWCKLNLDNVITVSIGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFNPPVLVF
Retrocopy RAMFSAIFAYDVEQWCKLNLDNVITVSIGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFNPPVLVF

Parental  VQSIERAKELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVINYD
          VQSIERAKELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVINYD
Retrocopy VQSIERAKELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVINYD

Parental  FPTSSVEYIHRIGRTGRAGHKGKAVTFFTEDDKPLLRSVANVIQQAGCPVPEYIKGFQKLLSKQKKKMIK
          FPTSSVEYIHRIGRTGRAGHKGKAVTFFTEDDKPLLRSVANVIQQAGCPVPEYIKGFQKLLSKQKKKMIK
Retrocopy FPTSSVEYIHRIGRTGRAGHKGKAVTFFTEDDKPLLRSVANVIQQAGCPVPEYIKGFQKLLSKQKKKMIK

Parental  KPLERESISTTPKYFLEKAKNKRKKVTAQNSKKKVTLEDKS
          KPLERESISTTPKYFLEKAKNKRKKVTAQNSKKKVTLEDKS
Retrocopy KPLERESISTTPKYFLEKAKNKRKKVTAQNSKKKVTLEDKS

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	0.42 RPM	7.85 RPM
SRP017611_brain	0.16 RPM	5.72 RPM
SRP017611_kidney	0.33 RPM	5.08 RPM
SRP017611_liver	0.22 RPM	2.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_51 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_51 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_51 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018145	1 retrocopy	retro_cfam_51 ,
Otolemur garnettii	ENSOGAG00000000868	1 retrocopy	retro_ogar_2655,