RetrogeneDB ID: retro_fcat_1639

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:65696077..65696557(-)
• Located in intron of: ENSFCAG00000018633

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000028482
• Aliases: None
• Description: None

Sequence

>retro_fcat_1639
ATGTGTTCCCACTTCAACCACGATGAAATTAAAAGGCTGAGCAAGAGGTTTAAGAAGCTGGACTTGGACTGTTCGGGCTC
TCTGAGCGTGGACGAGTTCTTGTCCCTGCCCGAGCTGCGGCAGAACCCGTTGGTGCAGCGAGTGATCGACGTCTTCGACA
CCGACGGCAATGGAGAGGTGGACTTTGAGGAGTTCGTCGTGGGGACCTCCCAGTTCAGCGTCAGGGGGGACGAGGAGCAG
AAGTTGAGGTTTGCCTTCAGCATCTACGACATGGATAAAGACGGCTACATTTCCAACGGGGAGCTGTTCCAGGTGCTGAA
GATGATGGTGGGGAACAACCTGCAAGACTGGCAGTTACAGCAGATCGTGGACAAAACCATCATCATCCTGGACAGGGATG
GCGACGGGAGAATATCCTTCGAGGAATTCAGTGCGGTGGTCGGAAACCTGGAGGTCCACAAGAAGTTGGTGGTAATTGTG

Alignment

ORF - retro_fcat_1639 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKEFIEGVS
          MCSHF..DEIKRL.KRFKKLDLD.SGSLSV.EF.SLPEL.QNPLVQRVID.FDTDGNGEVDF.EF..G.S
Retrocopy MCSHFNHDEIKRLSKRFKKLDLDCSGSLSVDEFLSLPELRQNPLVQRVIDVFDTDGNGEVDFEEFVVGTS

Parental  QFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISF
          QFSV.GD.EQKLRFAF.IYDMDKDGYISNGELFQVLKMMVGNNL.D.QLQQIVDKTII..D.DGDGRISF
Retrocopy QFSVRGDEEQKLRFAFSIYDMDKDGYISNGELFQVLKMMVGNNLQDWQLQQIVDKTIIILDRDGDGRISF

Parental  EEFCAVVGGLDIHKKMVVDV
          EEF.AVVG.L..HKK.VV.V
Retrocopy EEFSAVVGNLEVHKKLVVIV

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	152.19 RPM
SRP017611_kidney	0.00 RPM	13.50 RPM
SRP017611_liver	0.00 RPM	11.73 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1639 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1639 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.

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010619	1 retrocopy	retro_btau_1660,
Choloepus hoffmanni	ENSCHOG00000002893	1 retrocopy	retro_chof_2602,
Callithrix jacchus	ENSCJAG00000006498	1 retrocopy	retro_cjac_624,
Dipodomys ordii	ENSDORG00000019760	1 retrocopy	retro_dord_404,
Equus caballus	ENSECAG00000009627	1 retrocopy	retro_ecab_651,
Felis catus	ENSFCAG00000006346	1 retrocopy	retro_fcat_1964,
Felis catus	ENSFCAG00000028482	1 retrocopy	retro_fcat_1639 ,
Homo sapiens	ENSG00000221823	1 retrocopy	retro_hsap_3,
Loxodonta africana	ENSLAFG00000022682	1 retrocopy	retro_lafr_1014,
Macaca mulatta	ENSMMUG00000017460	1 retrocopy	retro_mmul_1141,
Mustela putorius furo	ENSMPUG00000006250	1 retrocopy	retro_mputfur_537,
Nomascus leucogenys	ENSNLEG00000026538	1 retrocopy	retro_nleu_1049,
Oryctolagus cuniculus	ENSOCUG00000027562	1 retrocopy	retro_ocun_272,
Otolemur garnettii	ENSOGAG00000034876	1 retrocopy	retro_ogar_1011,
Pan troglodytes	ENSPTRG00000041941	1 retrocopy	retro_ptro_2909,
Rattus norvegicus	ENSRNOG00000043210	1 retrocopy	retro_rnor_1932,
Sus scrofa	ENSSSCG00000022362	1 retrocopy	retro_sscr_86,
Ictidomys tridecemlineatus	ENSSTOG00000025985	1 retrocopy	retro_itri_1569,
Tarsius syrichta	ENSTSYG00000019531	2 retrocopies	retro_tsyr_326, retro_tsyr_41,
Tursiops truncatus	ENSTTRG00000021395	1 retrocopy	retro_ttru_382,
Vicugna pacos	ENSVPAG00000015522	1 retrocopy	retro_vpac_3,
Drosophila melanogaster	FBgn0015614	1 retrocopy	retro_dmel_53,