RetrogeneDB ID: retro_fcat_1140

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:159311111..159311579(+)
• Located in intron of: ENSFCAG00000012076

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS14
• Ensembl ID: ENSFCAG00000011085
• Aliases: None
• Description: Ribosomal protein S14 [Source:UniProtKB/TrEMBL;Acc:Q66TU2]

Sequence

>retro_fcat_1140
AGAAGACATGCGGAAATGGCACCTCTCAAGGGGAAGGAAAAGAAGGAAGAACAGGTCATCAGCCTCAGATCTCAAGTGGC
TGAAGGAGAAAATGTATTTGGTGTCCACCGCATCTTTGCATCCTTCAGTGACACTATTGTCCAGGTCACTGATCTTTCTG
GCAAGGAAACCATCTGCTGTGTGACTAGTGAGATGAAGGTGAAGGCTGACCGAGATGAGTCCTCTCCTTTTGCTGCCATG
TTGGCTGCCCAGGATGTAGCCCAAAGGTACAAGGAGCTGGGCACCGCTGCCCTCCACATCCAACTCCAGGCCACAGGAGC
AAATAGGACCAAGATCCCTGGCCCTGGAGCCCAGTCAACCCTCAGAGCCATTGTCCACTCAGGAATGAAGATCGGGCAGA
TTGAGGAAGCCACCCCCATCCCCTCTGATAGTACCTGCAGGAAGGGGGGTTGCTGTGGTCACCGTCTA

Alignment

ORF - retro_fcat_1140 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 97.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLSQEMAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKAD
          R...EMAP.KGKEKKEEQVISL..QVAEGENVFGV..IFASF.DT.V.VTDLSGKETIC.VT..MKVKAD
Retrocopy RRHAEMAPLKGKEKKEEQVISLRSQVAEGENVFGVHRIFASFSDTIVQVTDLSGKETICCVTSEMKVKAD

Parental  RDESSPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPI
          RDESSP.AAMLAAQDVAQR.KELG..ALHI.L.ATG.NRTK.PGPGAQS.LRA...SGMKIG.IE..TPI
Retrocopy RDESSPFAAMLAAQDVAQRYKELGTAALHIQLQATGANRTKIPGPGAQSTLRAIVHSGMKIGQIEEATPI

Parental  PSDSTRRKGGRRGRRL
          PSDST.RKGG..G.RL
Retrocopy PSDSTCRKGGCCGHRL

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	80.91 RPM
SRP017611_kidney	0.00 RPM	275.99 RPM
SRP017611_liver	0.00 RPM	122.93 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1140 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1140 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 15 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Cavia porcellus	ENSCPOG00000024408	2 retrocopies	retro_cpor_253, retro_cpor_284,
Felis catus	ENSFCAG00000011085	5 retrocopies	retro_fcat_1140 , retro_fcat_622, retro_fcat_670, retro_fcat_857, retro_fcat_925,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Loxodonta africana	ENSLAFG00000031195	2 retrocopies	retro_lafr_235, retro_lafr_67,
Myotis lucifugus	ENSMLUG00000013279	4 retrocopies	retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Rattus norvegicus	ENSRNOG00000018774	10 retrocopies	retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,