RetrogeneDB ID: retro_cfam_536

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:72193057..72193657(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ECI2
• Ensembl ID: ENSCAFG00000009409
• Aliases: ECI2, PECI
• Description: enoyl-CoA delta isomerase 2 [Source:HGNC Symbol;Acc:14601]

Sequence

>retro_cfam_536
AGCGCATCGACCGTGCGGATGTACCGGGAAACCTCGCCTGCTCGTGAAGCTGCGAGCCAGGAGGACCGTGCCACAGCTGT
CCTAACCGGAAATGGTGACTCCTACTCTGGTGGGAAGGATCTGAGGAATTTCATGGATATTCCCCTGGCGAAATAGAGGA
GGAAGCCAAGAATGGGGCCGTTTTACCGACGGACTTTGTAGGCCGTTTTCTAGCTTTTCCTAAGCCTCGGGTGCGTGGTG
AATGGTGCAGCCACGGGAATCTCCGTCACCGTTCCCAGGCTCCTCGGCCTTGTGTGTGCTTCCGACGGGGCAACATTTCA
CACTCCTTTTACTCACGTGGGCCAAAGTCCAGAAGGATGTTCCTCGTACACGTCCCCCAAGGTGATGGGCCAAGCCGAGG
CAGCCGGGGAGCTCACGTTTGGGAAGACGTCTCCAGCCAGAGAAGCCCGTGCTCCGGGGCTCGTTACTGAAGCTCCCGAT
GGCACTTTTCAGAAAGAGGTTTGGACCGGGCTGGAGGGATACTCAAAGCTCCCCCGAAGTGCCTTTTGCATATTTCAAAA
CAGAGCATCGGAAATCTCAAGAAAGCAGAGCTACGCGCTG

Alignment

ORF - retro_cfam_536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.46 %
• Parental protein coverage: 54.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NALTIQMYREIMLALEAASKDDSTIIVLTGNGDYYSSGNDLMNFMNIPPGEMEKEAKNGAILLRDFVGCF
          .A.T..MYRE...A.EAAS..D....VLTGNGD.YS.G.DL.NFM.IP..........G....R.....F
Retrocopy SASTVRMYRETSPAREAASQEDRATAVLTGNGDSYSGGKDLRNFMDIPLAK*RRKPRMGPFYRRTL*AVF

Parental  IDFPKPLVAVINGPAIGISVTILGLFDLVYASDRATFHTPFTHLGQSPEGCSSYTFPKIMGQAKAAEMLM
          ..F...L..V.NG.A.GISVT...L..LV.ASD.ATFHTPFTH.GQSPEGCSSYT.PK.MGQA.AA..L.
Retrocopy *LFLS-LGCVVNGAATGISVTVPRLLGLVCASDGATFHTPFTHVGQSPEGCSSYTSPKVMGQAEAAGELT

Parental  FGKKLTAREACAQGLVTEVFPDSTFQKEVWTRLKAYSKLPRNTLHISKQSIRNLEKEKLHAV
          FGK...AREA.A.GLVTE..PD.TFQKEVWT.L..YSKLPR....I..............A.
Retrocopy FGKTSPAREARAPGLVTEA-PDGTFQKEVWTGLEGYSKLPRSAFCIFQNRASEISRKQSYAL

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	0.84 RPM	17.30 RPM
SRP017611_brain	0.00 RPM	9.77 RPM
SRP017611_kidney	0.00 RPM	65.24 RPM
SRP017611_liver	0.00 RPM	97.31 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_536 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_536 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009409	1 retrocopy	retro_cfam_536 ,
Choloepus hoffmanni	ENSCHOG00000009239	1 retrocopy	retro_chof_25,
Procavia capensis	ENSPCAG00000008568	1 retrocopy	retro_pcap_71,
Rattus norvegicus	ENSRNOG00000016369	1 retrocopy	retro_rnor_1179,
Tupaia belangeri	ENSTBEG00000015862	2 retrocopies	retro_tbel_2398, retro_tbel_814,