RetrogeneDB ID: retro_fcat_1172

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:39302924..39303237(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000009408
• Aliases: None
• Description: None

Sequence

>retro_fcat_1172
GTGCCCACAGGACTGGTAGAGCGACTCGGCACAGCCAGTGCAGCCATCCGGGGCCAACCTGAAGACTATGTGAGCATGAT
GGTGTGACCAGGTCTGGCCTTGGTGGTGAACAGCTCCACTGAGCCCTGCGTGCAACTGCTCATCTCTTCCATCCCATGTG
GAGGACACTGCAGAGGAGAACTGCAGTCACAAAGCCCAATTCTTCAAGTCCCTCACCAAGGAGCTGGACCTGGGCCAGGA
TCCGATAATTATCTGCTTTCCCCCCCTGGAACCCTGGCAGATTGGCAAGAAAGGGACAGTCATGACTTTTCTA

Alignment

ORF - retro_fcat_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 88.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPAGLEKRLCAATAAILSKPEDRVNVTLRPGLAMAVNGSTDPCAQLIISSIGVVG-TAEENRGHSARFFE
          VP.GL..RL..A.AAI...PED.V.....PGLA..VN.ST.PC.QL.ISSI...G.TAEEN..H.A.FF.
Retrocopy VPTGLVERLGTASAAIRGQPEDYVSMMV*PGLALVVNSSTEPCVQLLISSIPCGG>TAEENCSHKAQFFK

Parental  FLTKEMGLGQDRIIIRFFPLEPWQIGKKGTVMTFL
          .LTKE..LGQD.III.F.PLEPWQIGKKGTVMTFL
Retrocopy SLTKELDLGQDPIIICFPPLEPWQIGKKGTVMTFL

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	3.56 RPM
SRP017611_kidney	0.00 RPM	31.95 RPM
SRP017611_liver	0.00 RPM	30.12 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1172 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1172 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013811	1 retrocopy	retro_amel_1024,
Callithrix jacchus	ENSCJAG00000009483	1 retrocopy	retro_cjac_2434,
Felis catus	ENSFCAG00000009408	1 retrocopy	retro_fcat_1172 ,
Macaca mulatta	ENSMMUG00000004552	1 retrocopy	retro_mmul_312,
Mustela putorius furo	ENSMPUG00000002935	1 retrocopy	retro_mputfur_1365,