RetrogeneDB ID: retro_fcat_1718

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E2:49942913..49943185(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000027510
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LAMTOR5
• Ensembl ID: ENSFCAG00000023792
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 5 [Source:HGNC Symbol;Acc:17955]

Sequence

>retro_fcat_1718
ATGGAGACGACCTTGGAGCAACACTTGGAGGACACAGTGAAGAATTCATCCATTGTTGGAGTCCTGTGCACAGATTCACA
AGGTCTTAATCTGGGCTGCCGCGGATCCCTGTCAGATGAGCATGCTGGGGTAACATCTGTTCTAGCCCAGCAAGCAGCTA
AGCTAACCGCAGTCCCCACTAAATTCCTGTGGTGTGTCTAGAATCAGATAATGGGAACATTATGATCCAGAAACATGATG
GCATCACAGTAGCGGAGCACAAAATGGTCTCT

Alignment

ORF - retro_fcat_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPTD-IPVVCLES
          ME.TLEQHLEDT.KN.SIVGVLCTDSQGLNLGCRG.LSDEHAGV.SVLAQQAAKLT..PT..IPVVCLES
Retrocopy METTLEQHLEDTVKNSSIVGVLCTDSQGLNLGCRGSLSDEHAGVTSVLAQQAAKLTAVPTK<IPVVCLES

Parental  DNGNIMIQKHDSITVAVHKMAS
          DNGNIMIQKHD.ITVA.HKM.S
Retrocopy DNGNIMIQKHDGITVAEHKMVS

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	15.84 RPM
SRP017611_kidney	0.00 RPM	31.43 RPM
SRP017611_liver	0.00 RPM	11.42 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1718 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1718 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 6 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011504	2 retrocopies	retro_amel_118, retro_amel_974,
Bos taurus	ENSBTAG00000014970	3 retrocopies	retro_btau_1505, retro_btau_1755, retro_btau_71,
Felis catus	ENSFCAG00000023792	5 retrocopies	retro_fcat_1718 , retro_fcat_1853, retro_fcat_1887, retro_fcat_413, retro_fcat_478,
Macaca mulatta	ENSMMUG00000015023	4 retrocopies	retro_mmul_164, retro_mmul_2452, retro_mmul_440, retro_mmul_499,
Sus scrofa	ENSSSCG00000006807	1 retrocopy	retro_sscr_986,
Ictidomys tridecemlineatus	ENSSTOG00000003401	5 retrocopies	retro_itri_1196, retro_itri_154, retro_itri_198, retro_itri_587, retro_itri_86,