RetrogeneDB ID: retro_cfam_2200

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:97191705..97192216(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSCAFG00000028683
• Aliases: None
• Description: mitochondrial ribosomal protein S25 [Source:HGNC Symbol;Acc:14511]

Sequence

>retro_cfam_2200
ATGCCCATGAAAGGTTTCTTCCTGATCTGCCACATCTTCCAGTACCTGGGCCAGGGGGAGATTGTGTTCAAAATCAGTGA
AGGTCATGACTGTGAACTACAACATGCATGGGTAGCTGAGCAAGAGCACTAGAAAATTTGTAATTTTCAACATACCTTAG
ATCCAGTACAAATATGTTGGGTACAGATCCTGATGTTTAAGAACATGATGCTGTCCCCATTTCTGTGGTTTTATCTGGAT
TCCAGAGAGTAGCTCCTCATAGATGTGGAGACCATGTGTAATAAACGGATTTGGAGCTCATCCTACAAATCTTGGAGAAG
AAGAAGGAAACTCTCAAAAAGAGGAATAGGAGAAAAAAACAGCTTTCTCACCCAGCCCACTTTGGCCCCCAAAAGTACTG
CCTGCTGAAGTTCCTCTGTATGGTGAAAGGGCAGGTCCCCTGCCAGAGCTGGTGGCATTACCCAAGGAGATGACAGCGAA
GTACAAAGCAACACCAAAAGCCAGGACTGAG

Alignment

ORF - retro_cfam_2200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 99.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPMKGRFPIRRTLQYLG-QGDVVFKDSVKVMTVNYNTHGELGEGARKFVFFNIPQIQYKNP-WVQIMMFK
          MPMKG.F.I....QYLG..G....K.SVKVMTVNYN.HG.L....RKFV.FNIP.IQYK...WVQI.MFK
Retrocopy MPMKGFFLICHIFQYLG>RGRLCSK-SVKVMTVNYNMHG*LSKSTRKFVIFNIP*IQYKYV<WVQILMFK

Parental  NMTPSPFLRFYLDSGEQVLVDVETKSNKEI-VEHIKKILGKNKETLEEEEQEKKQLSHPAHFGPRKYCLR
          NM..SPFL.FYLDS.E..L.DVET..NK.I..E.I..IL.K.KETL......KKQLSHPAHFGP.KYCL.
Retrocopy NMMLSPFLWFYLDSRE*LLIDVETMCNKRI<LELILQILEKKKETLKKRNRRKKQLSHPAHFGPQKYCLL

Parental  ECICEVEGQVPC-PGLLPLPKELTGKYKAMLTASTQ
          ...C.V.GQVPC.P.L..LPKE.T.KYKA...A.T.
Retrocopy KFLCMVKGQVPC<PELVALPKEMTAKYKATPKARTE

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	66.82 RPM
SRP017611_brain	0.00 RPM	37.79 RPM
SRP017611_kidney	0.00 RPM	60.89 RPM
SRP017611_liver	0.00 RPM	22.84 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2200 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2200 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004349	1 retrocopy	retro_amel_1861,
Canis familiaris	ENSCAFG00000028683	1 retrocopy	retro_cfam_2200 ,
Echinops telfairi	ENSETEG00000008261	2 retrocopies	retro_etel_1144, retro_etel_1227,
Felis catus	ENSFCAG00000027687	1 retrocopy	retro_fcat_2014,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Loxodonta africana	ENSLAFG00000022178	1 retrocopy	retro_lafr_1068,
Mustela putorius furo	ENSMPUG00000017248	1 retrocopy	retro_mputfur_1608,
Oryctolagus cuniculus	ENSOCUG00000006984	1 retrocopy	retro_ocun_1040,
Ochotona princeps	ENSOPRG00000009370	3 retrocopies	retro_opri_288, retro_opri_690, retro_opri_951,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Tursiops truncatus	ENSTTRG00000009881	1 retrocopy	retro_ttru_140,