RetrogeneDB ID: retro_cfam_1790

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:26409525..26409981(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOP16
• Ensembl ID: ENSCAFG00000016694
• Aliases: None
• Description: NOP16 nucleolar protein [Source:HGNC Symbol;Acc:26934]

Sequence

>retro_cfam_1790
ATGCCCAAGGCCAAGGGGAAGACCAGGAGACAAAAATTCGGTTACAATGTTAACCGGAAGAGTCTGAACCGGAATGCTTG
ACGGAAAGCAGCGCCACGGATTGAGTGTTCCCACATCCAACATGCCTGGGACCACGCTAAATCCGTGCGGCAGAACCTGG
CCGAGATGGGGTTGGCTATGGACCCCAACAAGGCAGTACCCCTCCAAAAGAGAAAGGTGAAGGCCATGGAGGTGGACATA
GAGGAGAGGCCTAAGGAGCTTGTGCGGAAGCCCTATGTGCTCAATGACCTAGAGGCAGAAGCCAGCCTCCCAGAAAAGAA
AGGAAACACACTGTCTCGAGACCTTATTGACTATGTGCACTACATGGTGGAGAATAACGGGGAGGACAAGGCTATGGCCC
GGGACGAGAAGAATTACTATCAAGATACCCCAAAACAGATTCGGAATAAGATCAAC

Alignment

ORF - retro_cfam_1790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.77 %
• Parental protein coverage: 85.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKAKGKTRRQKFGYNVNRKRLNRNARRKAAPRIECSHIRHAWDHAKSVRQNLAEMGLAVDPNKAVPLRK
          MPKAKGKTRRQKFGYNVNRK.LNRNA.RKAAPRIECSHI.HAWDHAKSVRQNLAEMGLA.DPNKAVPL.K
Retrocopy MPKAKGKTRRQKFGYNVNRKSLNRNA*RKAAPRIECSHIQHAWDHAKSVRQNLAEMGLAMDPNKAVPLQK

Parental  RKVKAMEVDIEERPKELVRKPYVLNDLEAEASLPEKKGNTLSRDLIDYVRYMVENHGEDYKAMARDEKNY
          RKVKAMEVDIEERPKELVRKPYVLNDLEAEASLPEKKGNTLSRDLIDYV.YMVEN.GED.KAMARDEKNY
Retrocopy RKVKAMEVDIEERPKELVRKPYVLNDLEAEASLPEKKGNTLSRDLIDYVHYMVENNGED-KAMARDEKNY

Parental  YQDTPKQIRNKIN
          YQDTPKQIRNKIN
Retrocopy YQDTPKQIRNKIN

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	8.65 RPM
SRP017611_brain	0.00 RPM	8.42 RPM
SRP017611_kidney	0.00 RPM	9.44 RPM
SRP017611_liver	0.00 RPM	9.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1790 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1790 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1790 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016694	2 retrocopies	retro_cfam_1790 , retro_cfam_1793,
Callithrix jacchus	ENSCJAG00000012315	1 retrocopy	retro_cjac_2208,
Echinops telfairi	ENSETEG00000010391	1 retrocopy	retro_etel_1329,
Mustela putorius furo	ENSMPUG00000012552	1 retrocopy	retro_mputfur_381,
Otolemur garnettii	ENSOGAG00000000824	2 retrocopies	retro_ogar_1323, retro_ogar_2299,
Rattus norvegicus	ENSRNOG00000017284	1 retrocopy	retro_rnor_2739,
Sus scrofa	ENSSSCG00000029577	1 retrocopy	retro_sscr_510,
Ictidomys tridecemlineatus	ENSSTOG00000004869	1 retrocopy	retro_itri_1124,