RetrogeneDB ID: retro_cfam_1838

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:19016192..19016777(+)
• Located in intron of: ENSCAFG00000013655

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT2
• Ensembl ID: ENSCAFG00000019569
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 2 [Source:HGNC Symbol;Acc:325]

Sequence

>retro_cfam_1838
CTGTTGCACCATCACACTAACATGGGGGAGAACATGAATATCATCTGTTGGTTTGACTAGCTCTTCAAGTACATTTAGGG
CCTTCACTCTGAGCCAGAGGGCCACCAGCAGCTGGAAGAGCACCATCCTTGTGTCATCATTTCTAACCACCAGAGTGTCC
TGAACTTGATGGGCCTCTTGGAGGCCCTCTGCAACTGCTGTGTGCAGATAGCCAAGCAGGGGTTCTCTTCATGGGCCTGT
AGGCCTGATCATGTGTCTCGGGAACGTCTTTATCAACTAGTAGTGCTCCAGGACAAACCATGACTGTGATGTCTGACGTG
GGCCAGTGCATGGTCAGAGAGAACCTCAAAATGTGGATTTACCCTGAGGATATCAGGACAGTGGGGACCTGTTACCTCAA
AGAACGATACCTTTTACCTGGCAATTCAGGTGTGGATGCCCATCATTTCTGTGGTATACCCCACCTTTGTTTCCTTCTAT
GACCCCAAAAGGAAAATGAAGTTCTTTATCTCAGGAATATTCAAAGTGGAGATGCCGGATGCCATCCCCACCAGTGGCCT
CATTATAACTGATGTCCCCAGGCTA

Alignment

ORF - retro_cfam_1838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.61 %
• Parental protein coverage: 71.53 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LLRHGGRSVENMRIIQWFVLSFKYVFGLRFEIKGRQKLELDHPCVIISNHQSILDMMGLMEALPERCVQI
          LL.H.....ENM.II.WF...FKY..GL..E..G.Q.LE..HPCVIISNHQS.L..MGL.EAL...CVQI
Retrocopy LLHHHTNMGENMNIICWFD*LFKYI*GLHSEPEGHQQLEEHHPCVIISNHQSVLNLMGLLEALCNCCVQI

Parental  AKRE-LLFLG-PVGLIMYLGGIFFINRQHSRT-AVTVMADVGERMVRENLKVWIY-PEGTRNDNGDLLP-
          AK....LF.G.PVGLIM.LG..F.IN...SRT...TVM.DVG..MVRENLK.WIY.P.G...D.GDLLP.
Retrocopy AKQG<VLFMG<PVGLIMCLGNVF-IN**CSRT>TMTVMSDVGQCMVRENLKMWIY<P*GYQ-DSGDLLP<

Parental  FKKGAFYLAIQTQVPIIPIVYSSFSSFYNPKTKL--FSSGTIRVEVLDAIPTSGLTVADVPKL
          .K...FYLAIQ...PII..VY..F.SFY.PK.K...F.SG...VE..DAIPTSGL...DVP.L
Retrocopy SKNDTFYLAIQVWMPIISVVYPTFVSFYDPKRKMKFFISGIFKVEMPDAIPTSGLIITDVPRL

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	2.23 RPM
SRP017611_brain	0.00 RPM	1.03 RPM
SRP017611_kidney	0.00 RPM	8.19 RPM
SRP017611_liver	0.00 RPM	33.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1838 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1838 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_825

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003965	1 retrocopy	retro_amel_982,
Canis familiaris	ENSCAFG00000019569	1 retrocopy	retro_cfam_1838 ,
Equus caballus	ENSECAG00000010932	1 retrocopy	retro_ecab_825,
Felis catus	ENSFCAG00000011607	1 retrocopy	retro_fcat_1778,
Mustela putorius furo	ENSMPUG00000011249	1 retrocopy	retro_mputfur_1160,
Ochotona princeps	ENSOPRG00000003291	1 retrocopy	retro_opri_578,
Ictidomys tridecemlineatus	ENSSTOG00000023422	1 retrocopy	retro_itri_5,