RetrogeneDB ID: retro_fcat_516

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:22298940..22299434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSFCAG00000029663
• Aliases: None
• Description: cyclin-dependent kinase 4 [Source:HGNC Symbol;Acc:1773]

Sequence

>retro_fcat_516
ATGGCTACTCCCCAGTATGAGCCAGTGGCTGAGATCGGTGTTGGTACCTATGGACACAAGGCCCATGGTCCCCACAGTGG
CCACTTTATGGCCCTCAAGAGTGTGAGAGTTCCTAATGGAAGAGTTGCTGGCGGGGGCCTTCCCATCAGCACAGTTCATG
AGGTGGCCTTACTGAGGCAGCTGGAAGCTTTTGAACATCCCAGTGTTGTCCACCTGATGGACCTTTGCGCCATGGCCCAA
ACTGCCTGAGAGACCAAAGTGACCCTGGTGTTTGAGCACATAGACCAAGACCAAAGGCTGTATCTGGACAAGGCCCCCCC
ACCAGGCTTGCCAGTGGAGACTATCAAGGAAATGATGCGCCAGTTCTAAGAGGCCTAGATTTCCTTCATGCCAACTGTAT
CATTCACTGAGATCTGAAGCCAGAGAGCATTCTGGTGACAAATGGTGGGACAGTCAAGTTGGCTGACTTTGGCCCGGCCA
GAATCTACAGCTAT

Alignment

ORF - retro_fcat_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.55 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATPRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGASGGLPISTVREVALLRRLEAFEHPN
          MATP.YEPVAEIGVG.YG...KA..PHSGHF.ALKSVRVPNG..A.GGLPISTV.EVALLR.LEAFEHP.
Retrocopy MATPQYEPVAEIGVGTYG--HKAHGPHSGHFMALKSVRVPNGRVAGGGLPISTVHEVALLRQLEAFEHPS

Parental  VVRLMDVCATARTDRETKVTLVFEHVDQDLRTYLDKAPPPGLPVETIKDLMRQF-LRGLDFLHANCIVHR
          VV.LMD.CA.A.T..ETKVTLVFEH.DQD.R.YLDKAPPPGLPVETIK..MRQF.LRGLDFLHANCI.H.
Retrocopy VVHLMDLCAMAQTA*ETKVTLVFEHIDQDQRLYLDKAPPPGLPVETIKEMMRQF<LRGLDFLHANCIIH*

Parental  DLKPENILVTSGGTVKLADFGLARIYSY
          DLKPE.ILVT.GGTVKLADFG.ARIYSY
Retrocopy DLKPESILVTNGGTVKLADFGPARIYSY

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	11.48 RPM
SRP017611_kidney	0.00 RPM	36.38 RPM
SRP017611_liver	0.00 RPM	17.59 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_516 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_516 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 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000014972	1 retrocopy	retro_fcat_329,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516 ,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,