RetrogeneDB ID: retro_fcat_1094

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:70118773..70119356(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRR3
• Ensembl ID: ENSFCAG00000025918
• Aliases: None
• Description: proline rich 3 [Source:HGNC Symbol;Acc:21149]

Sequence

>retro_fcat_1094
GCAGCCATTGCCGCAACCATGATGTTGAAACAAAAGAAGCAGAATTAGCAGCAGCAGCCACCACTGCAGCAGCCTCTGCT
GCCAGAGCGGAAAGAGACTGGAGACGAGGAGCATGGAAGTCCCATCGGACCACCCAGCATTCTGGGCCTTACTCCCGTGG
CCACTGGAAAGCCTGGTAACTCTAAGTCAGCTCTTCACAGAGGTCTTCCAGGGTCAAGGGGATGAATGATTCAACCACTG
CTGAGTCTCCCACCTCCTTCCTGGGGCAGAGGCCCAGTCTGGGGAGGCCTAGGCCCCAGGTGTGGCCCATGTGGTTGTGG
TTGGTGGAGGGCCAATACTGAACCTTTTTCCTGGACCAAGCCATGGAGGTCCTTTCAGAGGAGGCTTTCACAAAGAGCAG
AGAAGTCCTCGAAGGCTCAAAAGTTGGTCTCTTATCAAAAATACCTACCCACCCAAGTATGGCCCCTAAGTTATGGAAGA
CAAATCCTACCACCCTGTCTGCTGACATTTTGCCAAAAAGGGCCACTGTCGATATGAGGACCTCTGTGCCTTCTGCCATC
CAGGTGTCAATGGACCTCCTCTG

Alignment

ORF - retro_fcat_1094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.04 %
• Parental protein coverage: 90.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAIAATTMPKRKKQSQQQQPPLQQPPLPEREETGDEEDGSPIGPPSLLGPPPMANGKPGDPKSALHRGPP
          AAIAAT.M.K.KKQ..QQQPPLQQP.LPER.ETGDEE.GSPIGPPS.LG..P.A.GKPG..KSALHRG.P
Retrocopy AAIAATMMLKQKKQN*QQQPPLQQPLLPERKETGDEEHGSPIGPPSILGLTPVATGKPGNSKSALHRGLP

Parental  GSRGPMIPPLLSLPPPPRGRGPIRGGVGPRCGPYGRGWWGANTEPPF-PGPGHGGP-RGGFHKEQRNPRR
          GSRG.MI.PLLSLPPP..GRGP..GG.GPRCGP.G.G.W......PF.PGP.HGGP.RGGFHKEQR.PRR
Retrocopy GSRG*MIQPLLSLPPPSWGRGPVWGGLGPRCGPCGCG-WWRANTEPF>PGPSHGGPFRGGFHKEQRSPRR

Parental  LKSWSLI-NACPPKDGPQVMEDKSNRPVCRHFAKKGHCRYEDLCAFYHPGVNGPPL
          LKSWSLI.N..PPK.GP.VMEDKS..PVC.HFAKKGHCRYEDLCAF.HPGVNGPPL
Retrocopy LKSWSLIKNTYPPKYGP*VMEDKSYHPVC*HFAKKGHCRYEDLCAFCHPGVNGPPL

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	0.11 RPM	10.10 RPM
SRP017611_kidney	0.00 RPM	6.08 RPM
SRP017611_liver	0.00 RPM	3.74 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1094 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1094 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094 , retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308, retro_tsyr_841,