RetrogeneDB ID: retro_fcat_1778

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F1:22208656..22209009(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT2
• Ensembl ID: ENSFCAG00000011607
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 2 [Source:HGNC Symbol;Acc:325]

Sequence

>retro_fcat_1778
AATATCATCAGTTGCTTTGTCCAGCTCTTCAAGTACATATAGAACCCTTCACTTTGAGACAGAGGGCCACTAGAAGGTGG
AAGTGGGCCAACTCTGAGTCATCATTTTTTAACCACCAGAGTGTCCTGAACATGATAGGCCTGTTGGAGGCTCTCCACAA
GTGTTGCATGTAGATCACCAAGCAGGCATTCTCTTCATGGGGCCCATAGGCCTGATCATGTGTCTTGGGGACATCTTCAT
CAACTGGCAGTGCTCCAGGACAAACCATGACTCTGATGTCTGACATAGGCCAGCCCATGGTCATAGAGTACCTCAGAATG
TGGATCCACCCTGAGGACATGCAGAAGGATAAT

Alignment

ORF - retro_fcat_1778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.46 %
• Parental protein coverage: 53.88 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SIISWFVRTFKYVFG-LRFDIKGRQKLEVDHPCVIIS-NHQSILDMMGLMEALPKRCVQIAKRE-LLFMG
          .IIS.FV..FKY....L.F...G..K.EV....VII..NHQS.L.M.GL.EAL.K.C..I.K....LFMG
Retrocopy NIISCFVQLFKYI*N>LHFETEGH*KVEVGQL*VIIF>NHQSVLNMIGLLEALHKCCM*ITKQA<ILFMG

Parental  PVGLIMYLGGVFFINRQRSRT-AMTVMADVGERMVRENLKVWVYPEGTRNDN
          P.GLIM.LG...FIN.Q.SRT..MT.M.D.G..MV.E.L..W..PE....DN
Retrocopy PIGLIMCLGDI-FINWQCSRT>TMTLMSDIGQPMVIEYLRMWIHPEDMQKDN

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
SRP017611_brain	0.00 RPM	0.80 RPM
SRP017611_kidney	0.00 RPM	155.62 RPM
SRP017611_liver	0.00 RPM	53.48 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1778 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1778 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,