RetrogeneDB ID: retro_fcat_1443

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:57178001..57178464(-)
• Located in intron of: ENSFCAG00000007449

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSFCAG00000015355
• Aliases: None
• Description: ribosomal protein S10 [Source:HGNC Symbol;Acc:10383]

Sequence

>retro_fcat_1443
AGAAGAGCCATCTATGAACTCCTTTTCAAGGAGGGAAAGTGGTAGCCAAGAAGGAAGTCCACATGCCTAAACATCCTGAG
CTGGCAGACAAGAATGTGCCCAATCATAACATTATCAAGGCTATGCAGTCTCTCAAATCATAAGGCTACATAAAGGAATA
GTTTGCCTGGAGACATTTCTACAAGTACCTTATCAACAAGGTTATCCAGTATCTCTGTGAATACCCCCATCTGCCCCCTG
AGGTTGTGCCTGCCATTCTGCACCACATCCATCCTGAAACTGTCAGGCCATGGCCCAAAGGTGTGAGGGGAGAGCAACCT
GTAAGACTCACATGAGGGGAAGCTGACAGAGACACCTACAAAGCACTGTGCCCCCTGGTGCCAACAAGAAAGGTGAAGTT
GGGGCTGGGTCAGCAAGTGAATTCCAGTTTACAGGTGGATTTAGTCATGGATGTGGTCAGCCA

Alignment

ORF - retro_fcat_1443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.72 %
• Parental protein coverage: 94.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RIAIYELLFKEGV-MVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWYLTNEGI
          R.AIYELLFKEG...VAKK.VHMPKHPELADKNVPN....KAMQSLKS.GY.KE.FAWRHFY.YL.N..I
Retrocopy RRAIYELLFKEGK<VVAKKEVHMPKHPELADKNVPNHNIIKAMQSLKS*GYIKE*FAWRHFYKYLINKVI

Parental  QYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRSAVPPGADKKAEAG-AG
          QYL..Y.HLPPE.VPA.L....PET.RP.PKG..GE.P.RLT.GEADRDTY.....P.....K...G.AG
Retrocopy QYLCEYPHLPPEVVPAILHHIHPETVRPWPKGVRGEQPVRLT*GEADRDTY-KALCPLVPTRKVKLG<AG

Parental  SATEFQFRGGFGRGRGQP
          SA.EFQF.GGF..G.GQP
Retrocopy SASEFQFTGGFSHGCGQP

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	78.16 RPM
SRP017611_kidney	0.00 RPM	226.11 RPM
SRP017611_liver	0.00 RPM	126.16 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1443 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1443 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 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001047	4 retrocopies	retro_amel_1408, retro_amel_1706, retro_amel_446, retro_amel_890,
Canis familiaris	ENSCAFG00000001214	2 retrocopies	retro_cfam_1, retro_cfam_92,
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Felis catus	ENSFCAG00000015355	3 retrocopies	retro_fcat_1443 , retro_fcat_1681, retro_fcat_1757,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mustela putorius furo	ENSMPUG00000003117	3 retrocopies	retro_mputfur_1347, retro_mputfur_1533, retro_mputfur_1579,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Otolemur garnettii	ENSOGAG00000001365	5 retrocopies	retro_ogar_2166, retro_ogar_2314, retro_ogar_2553, retro_ogar_415, retro_ogar_873,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Rattus norvegicus	ENSRNOG00000000490	4 retrocopies	retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,