RetrogeneDB ID: retro_cfam_755

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:30665024..30665479(+)
• Located in intron of: ENSCAFG00000029666

Retrocopy information

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

Parental gene information

• Parental gene symbol: FIS1
• Ensembl ID: ENSCAFG00000013800
• Aliases: None
• Description: None

Sequence

>retro_cfam_755
ATGCAGGCCATACTGAACAAGTTGGTGTCTGTGGATGACCTGCTGAAGTTTGTTAAAGAAATTTCAAATCTGGGAAGGTA
GCAGGTTTCGTGTCCAAGAGCACACGGTTTGAGTATGGCTGGTGCCTGATGCAAAGCAAGTACAGCGATGACATCCGCAA
AGGCATTGCACTGCTAGAGTAGCTGCTCCCCAAAGGGAGTAAAGAGCAGTGGGCTTATGTCTTCTACCTGGCTATGGGGA
ACTACTGGCTCAAAGAATATGAGAAGGCACTAAAGCATGTGCGGGGGCTGCTGCAGACAGAGCCTCAGAACAACCAGGCC
CAGGAACTGGAATGGCTCACTGACAAGGCCAGGAAGAAAGATGGACTAGTGGACATGGCCATTGTTGGAGATGTGGCCCT
AGGCGTAGTGGACCTGGCTGGACTCATCCGACTTGCTGTATCCAAGTCCAAATCC

Alignment

ORF - retro_cfam_755 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEAVLNELVSVDDLLKFE-KKFQ-SEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIALLEELLPKGSKE
          M.A.LN.LVSVDDLLKF..KKFQ.S.K.AG.VSKST.FEY.WCL..SKY.DDIRKGIALLE.LLPKGSKE
Retrocopy MQAILNKLVSVDDLLKFV>KKFQ>SGKVAGFVSKSTRFEYGWCLMQSKYSDDIRKGIALLE*LLPKGSKE

Parental  EQRDYVFYLAVGNYRLKEYEKALKYVRGLLQTEPQNNQAKELERLIDKAMKKDGLVGMAIVGGMALGVAG
          .Q..YVFYLA.GNY.LKEYEKALK.VRGLLQTEPQNNQA.ELE.L.DKA.KKDGLV.MAIVG..ALGV..
Retrocopy -QWAYVFYLAMGNYWLKEYEKALKHVRGLLQTEPQNNQAQELEWLTDKARKKDGLVDMAIVGDVALGVVD

Parental  LAGLIGLAVSKSKS
          LAGLI.LAVSKSKS
Retrocopy LAGLIRLAVSKSKS

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	64.72 RPM
SRP017611_brain	0.00 RPM	49.78 RPM
SRP017611_kidney	0.07 RPM	150.76 RPM
SRP017611_liver	0.15 RPM	39.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_755 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_755 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_755 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	ENSCAFG00000013800	2 retrocopies	retro_cfam_557, retro_cfam_755 ,
Callithrix jacchus	ENSCJAG00000016053	1 retrocopy	retro_cjac_1913,
Loxodonta africana	ENSLAFG00000020494	1 retrocopy	retro_lafr_702,
Myotis lucifugus	ENSMLUG00000024207	1 retrocopy	retro_mluc_168,
Monodelphis domestica	ENSMODG00000005034	1 retrocopy	retro_mdom_1773,
Otolemur garnettii	ENSOGAG00000028158	1 retrocopy	retro_ogar_1544,
Rattus norvegicus	ENSRNOG00000001420	2 retrocopies	retro_rnor_1659, retro_rnor_1689,
Sus scrofa	ENSSSCG00000027757	1 retrocopy	retro_sscr_1083,