RetrogeneDB ID: retro_cfam_557

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:51156007..51156237(+)
• Located in intron of: None

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_557
AAGGATTTGGTCTTCTTCCTGGCTGTGGGGAGCGACCTGCTCAAGGAATACAAGATACCCTAAAGTACGTGAGGGGACTG
CTGTAGACCCAGCCCCTGAACATCCAGGCCGAGGAACTGGAATGGCTCATTAACAAGGCCGTGAGGAAGATGGAAACTGT
TGGAGACATGACCCTGGGTGCGAGGGGCCTGGCTGGACTCACTGGACTTGCTGTATCCAAGTGCAAGACC

Alignment

ORF - retro_cfam_557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.63 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDYVFYLAVGNYRLKEY-EKALKYVRGLLQTEPQNNQAKELERLIDKAMKKDGLVGMAIVGGMALGVAGL
          .D.VF.LAVG...LKEY....LKYVRGLL.T.P.N.QA.ELE.LI.KA..K...VG....G..A.G.AGL
Retrocopy KDLVFFLAVGSDLLKEY<QDTLKYVRGLL*TQPLNIQAEELEWLINKAVRKMETVGDMTLG--ARGLAGL

Parental  AGLIGLAVSKSKS
          .GL...AVSK.K.
Retrocopy TGL---AVSKCKT

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	0.00 RPM	150.76 RPM
SRP017611_liver	0.00 RPM	39.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_557 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_557 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,