RetrogeneDB ID: retro_fcat_1907

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:40086117..40086660(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000030626
• Aliases: None
• Description: None

Sequence

>retro_fcat_1907
ATGGCAACTGGACTGAAATTGATGAGAGCAATTGGAGTTGTTGAATTTGGTGGACCAGAGTGCTGAAACTCCAGTCGGGA
TGTGGCAGTACCAACTCCAAAAGACCATCAGGTTGTAATCAAGGTCCATGCATGTGGTGTAAACCCAGTGGAAACATAGA
TTCGTTCTGCTACTCACAGGATAAAACCACTCTTACCCTATACTCCTGGTTCAGACGTGGCTGGGGTAACAGAAGCTGTT
GGACGTAACGTATCTACTTTCAAGAAAGGTGACGGAGTTTTCACTCCCAGCACCATCTCTGGGGGCTATGCTGAGTATGC
TCTTGCGGCAGACCACACTGTGTACCCACCGTCAGAAAAACTGGACTTTAAACAAGGAGCTGCCATCGGTATCCCATATT
TTACTGCTTATCGAGCTCTGCTCCACAGCGCCCGTGTGAAAGCTGGAGGAAGTGTTCGGGTTCATGGGGCTAGTGGAGGA
GTTGGATTGGCCGTATGCCAGACTGCCAGAGCTTATGGTTTAAAGGTTCTGGGCACAGCCGGC

Alignment

ORF - retro_fcat_1907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 55.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATGLKLMRAIRVFEFGGPE-VLKLQS-DVAVPTPKDHQVLIKVHACGVNPVETYIRSGTHKIKPLLPYT
          MATGLKLMRAI.V.EFGGPE.VLKLQS.DVAVPTPKDHQV.IKVHACGVNPVET.IRS.TH.IKPLLPYT
Retrocopy MATGLKLMRAIGVVEFGGPE<VLKLQS>DVAVPTPKDHQVVIKVHACGVNPVET*IRSATHRIKPLLPYT

Parental  PGSDVAGVIEAVGDNASTFKKGDRVFTTSTISGGYAEYALAADHTVYPLPEKLDFKQGAAIGIPYFTAYR
          PGSDVAGV.EAVG.N.STFKKGD.VFT.STISGGYAEYALAADHTVYP..EKLDFKQGAAIGIPYFTAYR
Retrocopy PGSDVAGVTEAVGRNVSTFKKGDGVFTPSTISGGYAEYALAADHTVYPPSEKLDFKQGAAIGIPYFTAYR

Parental  ALLHSARVKAGESVLVHGASGGVGLAVCQIARAYGLKVLGTAG
          ALLHSARVKAG.SV.VHGASGGVGLAVCQ.ARAYGLKVLGTAG
Retrocopy ALLHSARVKAGGSVRVHGASGGVGLAVCQTARAYGLKVLGTAG

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	0.57 RPM	14.58 RPM
SRP017611_kidney	0.41 RPM	70.70 RPM
SRP017611_liver	1.01 RPM	64.09 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1907 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1907 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 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003162	1 retrocopy	retro_btau_1433,
Canis familiaris	ENSCAFG00000020404	1 retrocopy	retro_cfam_870,
Choloepus hoffmanni	ENSCHOG00000005167	1 retrocopy	retro_chof_1772,
Felis catus	ENSFCAG00000030626	1 retrocopy	retro_fcat_1907 ,
Homo sapiens	ENSG00000116791	1 retrocopy	retro_hsap_3884,
Loxodonta africana	ENSLAFG00000011371	1 retrocopy	retro_lafr_527,
Macaca mulatta	ENSMMUG00000014593	2 retrocopies	retro_mmul_1026, retro_mmul_1728,
Mustela putorius furo	ENSMPUG00000010969	1 retrocopy	retro_mputfur_119,
Mus musculus	ENSMUSG00000028199	1 retrocopy	retro_mmus_1314,
Nomascus leucogenys	ENSNLEG00000009543	2 retrocopies	retro_nleu_1890, retro_nleu_3115,
Otolemur garnettii	ENSOGAG00000011586	1 retrocopy	retro_ogar_179,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165,
Pan troglodytes	ENSPTRG00000000865	1 retrocopy	retro_ptro_1598,
Tupaia belangeri	ENSTBEG00000016750	3 retrocopies	retro_tbel_1665, retro_tbel_2353, retro_tbel_3800,
Tarsius syrichta	ENSTSYG00000004193	2 retrocopies	retro_tsyr_1218, retro_tsyr_1884,
Tursiops truncatus	ENSTTRG00000010471	2 retrocopies	retro_ttru_555, retro_ttru_958,