RetrogeneDB ID: retro_cfam_797

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:21159278..21159712(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCFD2
• Ensembl ID: ENSCAFG00000032480
• Aliases: None
• Description: multiple coagulation factor deficiency 2 [Source:HGNC Symbol;Acc:18451]

Sequence

>retro_cfam_797
ACCATGAGATCTCAGTGGCTGCTCAGAACCCCTTCCTATGTGGTCTACTCCAGGCTGTTTGAGCTCCAGGTGCCAGACTG
AGGAGCCTGGAGCGAGCTTCTCCCATCCTGGCAGCATGGGCCTGGATGAGAATATAGTGCACGATCAAGAACATACCATG
AAGCATCTAAAAGATGTCATTAACAAACCAGAGATGGAGATGTCTTCACAAAAACTGCAGCTCTGTTATTTAAAATGCTT
GATTATGATGGCGATAATTTATGGGATGGCCTAGACTTTTCCATAGCCATCACTTGGGTCCATTAAGACAAAGAGAATGA
ATAGACACCACCAAAGAGTGAAGCTGAGCTGATTAACTTGATGGGGTTTTGAGAAAGAAAGATAAGAACAATAATAAATA
CATTGACCATGTTGAATTTGCAAAATCACTGCGG

Alignment

ORF - retro_cfam_797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.89 %
• Parental protein coverage: 85.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TMRSLWLLRTP-FLCGLLWAFRAPGAG-AEEPGASFSHPGSVGLDKNTVHDQEHIMEHLEGVINKPEAEM
          TMRS.WLLRTP.FLCGLL.A..APGA...EEPGASFSHPGS.GLD.N.VHDQEH.M.HL..VINKPE.EM
Retrocopy TMRSQWLLRTP<FLCGLLQAV*APGAR<TEEPGASFSHPGSMGLDENIVHDQEHTMKHLKDVINKPEMEM

Parental  SPQELQLHY-FKMHDYDGNNLLDGLELSTAITHVH-KEEGKQAPPVSEAELINLI-DGVLRDDDKNNDGY
          S.Q.LQL.Y.FKM.DYDG.NL.DGL..S.AIT.VH...E....PP.SEAELINL........D..NN..Y
Retrocopy SSQKLQLCY<FKMLDYDGDNLWDGLDFSIAITWVH*DKENE*TPPKSEAELINLM<GVLRKKDKNNNK-Y

Parental  IDYAEFAKSLQ
          ID..EFAKSL.
Retrocopy IDHVEFAKSLR

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	35.87 RPM
SRP017611_brain	0.00 RPM	45.97 RPM
SRP017611_kidney	0.00 RPM	200.75 RPM
SRP017611_liver	0.00 RPM	148.43 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_797 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_797 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_797 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006097	2 retrocopies	retro_amel_720, retro_amel_906,
Canis familiaris	ENSCAFG00000032480	1 retrocopy	retro_cfam_797 ,
Choloepus hoffmanni	ENSCHOG00000003286	6 retrocopies	retro_chof_110, retro_chof_1840, retro_chof_2447, retro_chof_3, retro_chof_41, retro_chof_581,
Felis catus	ENSFCAG00000009220	1 retrocopy	retro_fcat_42,
Macropus eugenii	ENSMEUG00000010002	1 retrocopy	retro_meug_2119,
Mustela putorius furo	ENSMPUG00000012043	1 retrocopy	retro_mputfur_885,
Sus scrofa	ENSSSCG00000021325	2 retrocopies	retro_sscr_1129, retro_sscr_422,
Ictidomys tridecemlineatus	ENSSTOG00000003692	1 retrocopy	retro_itri_1118,
Vicugna pacos	ENSVPAG00000010692	1 retrocopy	retro_vpac_368,