RetrogeneDB ID: retro_cfam_718

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:4494522..4495167(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FRG1
• Ensembl ID: ENSCAFG00000007135
• Aliases: None
• Description: FSHD region gene 1 [Source:HGNC Symbol;Acc:3954]

Sequence

>retro_cfam_718
CAACTTGATATTGTTGTAATCTTGTGGGTCACAACAAACTTTGGTGAAATTTCAAGGATGATAGCAATTGAAATGGATAA
AGGAACCTATATACATACATTGACAGTGGACTTTTTACACTGGGAGCGCCACATAAAGAAGTTTATGATGGCTAGTCTTC
CAGAACAGTTTACAGCTGTCATCCTGCCTCATTCCTGAATTGTGTTGAAATCTGGCTATGGAAAATATGTTGGTATCAAT
TCAGATGGACTTCTGGTGCATTTGGATATAATTGGACCAAGAGAACAATGGGAATTCGTCTTTCAAGATGAGAAAATGGC
TTTATTGACCTCAAATAGCTGCTTTATTAGATGCAATGAAGCAGAAAATATGGAACCAAAAGGTAAAACATCAGGAGAAG
AAGAAATGATAAAGATCAGATTCTGTGCTGAAAGAGAAACTAAGAAAAAAAAAGGTGATATTCCAGTGGAAGACAAAAGA
AATATTAAACAGTGTGTAATCAATTGTATAAAGAAATTTCAGAGCTTCCAAGATCATAAACCTAAAATAAAGACAATAAA
ATTTTCAAAAAGCCCAGAAAGATGTATTTTTGCATCAAACACTCTGGACAAGAGAGCAGAATTGAAAGCTAATAGATACT
GCAAA

Alignment

ORF - retro_cfam_718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.37 %
• Parental protein coverage: 84.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLDIVGIWWTVTNFGEISGTIAIEMDKGTYIHAL-DNGLFTLGAPHKEVDEGPS-PPEQFTAVKLSDSRI
          QLDIV.I.W..TNFGEIS..IAIEMDKGTYIH.L.D.GLFTLGAPHKEV..G.S.P...FTAV.L..S.I
Retrocopy QLDIVVILWVTTNFGEISRMIAIEMDKGTYIHTL<DSGLFTLGAPHKEVYDG*S>PEQ-FTAVILPHS*I

Parental  ALKSGYGKYLGINSDGLVVGRSDAIGPREQWEPVFQDGKMALLASNSCFIRCNEAGDIEAKSKTAGEEEM
          .LKSGYGKY.GINSDGL.V...D.IGPREQWE.VFQD.KMALL.SNSCFIRCNEA...E.K.KT.GEEEM
Retrocopy VLKSGYGKYVGINSDGLLV-HLDIIGPREQWEFVFQDEKMALLTSNSCFIRCNEAENMEPKGKTSGEEEM

Parental  IKIRSCAERETK-KKDDIPEEDKGNVKQCEINYVKKFQSFQDHKLKISKEDSKILKKARKDGFLHETLLD
          IKIR.CAERETK....DIP.EDK.N.KQC.IN..KKFQSFQDHK.KI.....K..K......F...T.LD
Retrocopy IKIRFCAERETKXXXGDIPVEDKRNIKQCVINCIKKFQSFQDHKPKI--KTIKFSKSPERCIFASNT-LD

Parental  RRAKLKADRYCK
          .RA.LKA.RYCK
Retrocopy KRAELKANRYCK

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	24.32 RPM
SRP017611_brain	0.00 RPM	14.61 RPM
SRP017611_kidney	0.00 RPM	23.05 RPM
SRP017611_liver	0.00 RPM	6.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_718 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_718 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013503	1 retrocopy	retro_amel_1609,
Canis familiaris	ENSCAFG00000007135	1 retrocopy	retro_cfam_718 ,
Felis catus	ENSFCAG00000025737	1 retrocopy	retro_fcat_464,
Myotis lucifugus	ENSMLUG00000023179	2 retrocopies	retro_mluc_1185, retro_mluc_1490,
Rattus norvegicus	ENSRNOG00000009846	1 retrocopy	retro_rnor_88,
Sorex araneus	ENSSARG00000002471	1 retrocopy	retro_sara_368,
Tupaia belangeri	ENSTBEG00000014491	2 retrocopies	retro_tbel_1202, retro_tbel_3435,
Tarsius syrichta	ENSTSYG00000010985	2 retrocopies	retro_tsyr_1347, retro_tsyr_1778,