RetrogeneDB ID: retro_fcat_142

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:600852..601098(+)
• Located in intron of: ENSFCAG00000031561

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR1
• Ensembl ID: ENSFCAG00000005320
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 [Source:HGNC Symbol;Acc:26068]

Sequence

>retro_fcat_142
GACCCCAGCAGCCCTCCTTCCAAAGCCCCCAGTGGAGCTGAGCCCAACTAACACAGCCTGCCTTCCGCTCGCACAGAGCA
GCAGGGCCCTGTACTCCTCACCCTTGCTAAAACAGCCGGTAACATCATTGCTGAGTCTGCTGTGGACTCCCATGGCGGGG
AGTAGCAGGAGGATGTGGGCCCGCCAAGGCAGTATGGTGCCTGCCTGCCTGGGCTGGGCAGCAGCCTGGACCACAGGAAG
AGGCTG

Alignment

ORF - retro_fcat_142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.32 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DPSSPPTKALNGAEPNYHSLPSTRTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLA
          DPSSPP.KA..GAEPN.HSLPS.RT..Q......LAKTA.NII..SA.DS.G.E..E.....RQY...L.
Retrocopy DPSSPPSKAPSGAEPN*HSLPSARTEQQGPVLLTLAKTAGNIIAESAVDSHGGE*QEDVGPPRQYGACLP

Parental  VLSSSLTHWKKL
          .L.SSL.H.K.L
Retrocopy GLGSSLDHRKRL

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	23.99 RPM
SRP017611_kidney	0.00 RPM	28.75 RPM
SRP017611_liver	0.00 RPM	12.23 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_142 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_142 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010854	2 retrocopies	retro_amel_1176, retro_amel_436,
Canis familiaris	ENSCAFG00000005788	1 retrocopy	retro_cfam_1962,
Echinops telfairi	ENSETEG00000010979	1 retrocopy	retro_etel_1005,
Felis catus	ENSFCAG00000005320	2 retrocopies	retro_fcat_142 , retro_fcat_496,
Macropus eugenii	ENSMEUG00000003560	1 retrocopy	retro_meug_17,
Myotis lucifugus	ENSMLUG00000014117	1 retrocopy	retro_mluc_2372,
Mustela putorius furo	ENSMPUG00000010289	3 retrocopies	retro_mputfur_1178, retro_mputfur_270, retro_mputfur_455,
Tarsius syrichta	ENSTSYG00000014730	2 retrocopies	retro_tsyr_1324, retro_tsyr_33,