RetrogeneDB ID: retro_fcat_296

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:213314468..213314888(-)
• Located in intron of: ENSFCAG00000000354

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL23
• Ensembl ID: ENSFCAG00000014502
• Aliases: None
• Description: ribosomal protein L23 [Source:HGNC Symbol;Acc:10316]

Sequence

>retro_fcat_296
ATGTTGAAGTGAGGATGTGGTGGGTCCTTCAGTGTGAAATTCTGGATTTCCCTAGGTCTTCTAGTAGGAGCCATGATCAA
CTGTGCTGACAACACAGGAACCAAAAAACCGTGTATCATCTCTGTGAAGGAGATCAAGCAACGACTGAACAGACTTTTCA
CTGCTGTTGTGGGTGACATGGTGATGGCCACAGTGAAGAAAGGCAAACCAGAGTTCAGAAAGAAGGTACAACCAGCAGTG
GTAATTTGTCAATGAAGGTCATACCAGAGAAAAGATGGTGTGTTTTTCTATTTTGAAGATAACAGAAGGGTCACAGTAAA
CAATAAAGGTGAAATGATAGGTTCTGCTATCACAGGAGGAGCTGCCAAAGAGTGTGCAGACTTGTGGCCCAGGATTTCAT
CCAATGCTGGCAGTATTGCA

Alignment

ORF - retro_fcat_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDMVMATVKKGKP
          M.K.G.GGS...KF.ISLGL.VGA.INCADNTG.K...IISVK.IK.RLNRL..A.VGDMVMATVKKGKP
Retrocopy MLK*GCGGSFSVKFWISLGLLVGAMINCADNTGTKKPCIISVKEIKQRLNRLFTAVVGDMVMATVKKGKP

Parental  ELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWPRIASNAGSIA
          E.RKKV.PAVVI.Q..SY.RKDGVF.YFEDN..V.VNNKGEM.GSAITG..AKECADLWPRI.SNAGSIA
Retrocopy EFRKKVQPAVVICQ*RSYQRKDGVFFYFEDNRRVTVNNKGEMIGSAITGGAAKECADLWPRISSNAGSIA

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	82.18 RPM
SRP017611_kidney	0.00 RPM	394.09 RPM
SRP017611_liver	0.10 RPM	158.31 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_296 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_296 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 13 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004268	6 retrocopies	retro_amel_1791, retro_amel_226, retro_amel_308, retro_amel_880, retro_amel_918, retro_amel_990,
Callithrix jacchus	ENSCJAG00000008311	9 retrocopies	retro_cjac_1129, retro_cjac_1483, retro_cjac_2283, retro_cjac_2598, retro_cjac_2639, retro_cjac_2772, retro_cjac_2885, retro_cjac_3128, retro_cjac_3831,
Dipodomys ordii	ENSDORG00000001372	3 retrocopies	retro_dord_366, retro_dord_475, retro_dord_530,
Felis catus	ENSFCAG00000014502	10 retrocopies	retro_fcat_1022, retro_fcat_1431, retro_fcat_1707, retro_fcat_1708, retro_fcat_1959, retro_fcat_242, retro_fcat_296 , retro_fcat_716, retro_fcat_756, retro_fcat_859,
Homo sapiens	ENSG00000125691	9 retrocopies	retro_hsap_2211, retro_hsap_2213, retro_hsap_2522, retro_hsap_3581, retro_hsap_3708, retro_hsap_3710, retro_hsap_4042, retro_hsap_4106, retro_hsap_556,
Latimeria chalumnae	ENSLACG00000004430	1 retrocopy	retro_lcha_16,
Macaca mulatta	ENSMMUG00000004502	9 retrocopies	retro_mmul_1598, retro_mmul_1705, retro_mmul_1955, retro_mmul_2366, retro_mmul_2391, retro_mmul_384, retro_mmul_928, retro_mmul_930, retro_mmul_935,
Nomascus leucogenys	ENSNLEG00000000642	7 retrocopies	retro_nleu_1506, retro_nleu_181, retro_nleu_2056, retro_nleu_2337, retro_nleu_2988, retro_nleu_574, retro_nleu_8,
Oryctolagus cuniculus	ENSOCUG00000013915	6 retrocopies	retro_ocun_1027, retro_ocun_1196, retro_ocun_1270, retro_ocun_1919, retro_ocun_251, retro_ocun_482,
Otolemur garnettii	ENSOGAG00000012445	7 retrocopies	retro_ogar_1050, retro_ogar_1645, retro_ogar_1695, retro_ogar_2250, retro_ogar_277, retro_ogar_3145, retro_ogar_539,
Ochotona princeps	ENSOPRG00000001957	10 retrocopies	retro_opri_1079, retro_opri_1216, retro_opri_137, retro_opri_14, retro_opri_178, retro_opri_202, retro_opri_224, retro_opri_481, retro_opri_639, retro_opri_684,
Rattus norvegicus	ENSRNOG00000004107	10 retrocopies	retro_rnor_1195, retro_rnor_1539, retro_rnor_1622, retro_rnor_2445, retro_rnor_2483, retro_rnor_2688, retro_rnor_2981, retro_rnor_347, retro_rnor_498, retro_rnor_941,
Ictidomys tridecemlineatus	ENSSTOG00000014279	2 retrocopies	retro_itri_122, retro_itri_1577,