RetrogeneDB ID: retro_cfam_1793

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:43272156..43272689(+)
• 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_1793
ATGCCCATGGCCAAGGGGAAGACCAGGAGACAGAAGTTTGGTTACAGTGTTAAATGGGAGCATCTGAACCGGAATGCTTG
ATGCAAAGCAGCTCCACTGATCGAGTGTTTCCACATCCGACATGCCTGGGACCATGGCAAATCCGTGCAGCAGAACCTGG
CAGAGATGGGGTTGGCTATGGACCCCAACAAGGAGGTGCCCCTCTGTAAGACAAAGGTGAGGCCATGCCAAGGAGGTGGA
CATGGAGGAGAGGCCTAAGATGCTTGTGCAGAAGCCCTATGTGCTAAGTGATCTAGAGGCAGAAGCCAGCCTCCCAGGAA
AGAAAGGAAGCACTGTCTGGAGACCTCATTGTCTATGTGGGCTACATGGTGGAGAATCACGGGGAGGACCATAAGGCTAT
GGCCCGGGTTGAGAAAAATTACTATCAAGATACTCCAAAACAGATTCGGAATAAGATCAATGTTTATAAGCATTTTTACC
TAGCAGAGCAGCAAGTCTTCATTGATTTTTTGCAGAATAAGATGGAGGTTGAG

Alignment

ORF - retro_cfam_1793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKAKGKTRRQKFGYNVNRKRLNRNARRKAAPRIECSHIRHAWDHAKSVRQNLAEMGLAVD-PNKAVP-L
          MP.AKGKTRRQKFGY.V....LNRNA..KAAP.IEC.HIRHAWDH.KSV.QNLAEMGLA.D.P....P..
Retrocopy MPMAKGKTRRQKFGYSVKWEHLNRNA*CKAAPLIECFHIRHAWDHGKSVQQNLAEMGLAMD>PTRRCPSV

Parental  RKRKVKAMEVDIEERPKELVRKPYVLNDLEAEASLP-EKKGNTLSRDLIDYVRYMVENHGEDYKAMARDE
          R.R...A.EVD.EERPK.LV.KPYVL.DLEAEASLP.E.K...LS.DLI.YV.YMVENHGED.KAMAR.E
Retrocopy RQR*GHAKEVDMEERPKMLVQKPYVLSDLEAEASLP>ERK-EALSGDLIVYVGYMVENHGEDHKAMARVE

Parental  KNYYQDTPKQIRNKINVYRRFYPAEWQTFTESLQKNKMEVE
          KNYYQDTPKQIRNKINVY..FY.AE.Q.F...LQ.NKMEVE
Retrocopy KNYYQDTPKQIRNKINVYKHFYLAEQQVFIDFLQ-NKMEVE

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_1793 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1793 has 0 orthologous retrocopies within eutheria group .

---

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,