RetrogeneDB ID: retro_fcat_421

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:28765700..28766093(+)
• Located in intron of: ENSFCAG00000007379

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD8
• Ensembl ID: ENSFCAG00000023811
• Aliases: None
• Description: COMM domain containing 8 [Source:HGNC Symbol;Acc:26036]

Sequence

>retro_fcat_421
CCCTTGTGGCAGCTGCAGAAGCTTCCAGCAGAGGTGGGCCTGCAGCTTCTTCACAAAATAATTGATAGCATTTGTAGCCG
AGCTTATCCTCTCTACCAGGATTCGCGCTGTGTTTGGGATTCAACAGAATGGAAGAATGTTCTAGAAGATATTACCAAAT
TTTTCAAAGCTGTAGTTGGTAAAAATTTACCTGATGAAGAGATATTTCAGCAGTTGAATCAGCTGAATTAATTTCATCAA
GAAGCTATCATGAAATGCTTAAAAAGTAGGAAAAGATGAAATCAGGCAGGCTCTGTTACAAGAAATAGTTGATATTTCTT
CTCACAGCTACAGGATTTTGATTGGCAGTTAAAGCTTGCATCGTCTAGTAACAAGATTGCTACGTTATAAATG

Alignment

ORF - retro_fcat_421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 71.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLYSFNKTQISPGKELLHKIIDGICGRAYPLYQDYHSVWDSTEWKNVLEDITKFFKAVVGKNLPDEEIFQ
          PL....K.....G..LLHKIID.IC.RAYPLYQD...VWDSTEWKNVLEDITKFFKAVVGKNLPDEEIFQ
Retrocopy PLWQLQKLPAEVGLQLLHKIIDSICSRAYPLYQDSRCVWDSTEWKNVLEDITKFFKAVVGKNLPDEEIFQ

Parental  QLNQLNSFHQEAIMKCLKSR-KEEIKKALFEEIVDISS-AQLQDFDWQLKLALSSDKIATLQM
          QLNQLN.FHQEAIMKCLKSR.K.EI..AL..EIVDISS..QLQDFDWQLKLA.SS.KIATL.M
Retrocopy QLNQLN*FHQEAIMKCLKSR>KDEIRQALLQEIVDISS<SQLQDFDWQLKLASSSNKIATL*M

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	22.38 RPM
SRP017611_kidney	0.10 RPM	20.20 RPM
SRP017611_liver	0.10 RPM	9.10 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_421 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_421 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001348	1 retrocopy	retro_btau_579,
Echinops telfairi	ENSETEG00000020257	3 retrocopies	retro_etel_1416, retro_etel_182, retro_etel_210,
Felis catus	ENSFCAG00000023811	1 retrocopy	retro_fcat_421 ,
Myotis lucifugus	ENSMLUG00000011376	1 retrocopy	retro_mluc_1158,
Macaca mulatta	ENSMMUG00000021777	1 retrocopy	retro_mmul_434,
Ochotona princeps	ENSOPRG00000000739	1 retrocopy	retro_opri_805,
Ictidomys tridecemlineatus	ENSSTOG00000001221	1 retrocopy	retro_itri_1566,