RetrogeneDB ID: retro_fcat_1684

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E2:12959524..12959844(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSFCAG00000030207
• Aliases: None
• Description: signal recognition particle 14kDa (homologous Alu RNA binding protein) [Source:HGNC Symbol;Acc:11299]

Sequence

>retro_fcat_1684
ATGGTGCTGCTGGAGAGCAACCACTTCCTGATGAAGCTGACCAGATTCTTCTAGAAGTGCTGTTTGTCATGCAGCGTGCT
GATCACCCTGAAGAAGTATGATGGTCAGACTAAACCCATTCCAAGGAAAGTTCTGCGGAGGGCTGCGAGCCCTCGGACAG
CAAGTGTCTGTTAAGAGCTACTGATGGCAAAGGTTAGCACTGTGGTGTGCTCCCGAAGAAGCGAACAGGTTTCAGGTGGC
TCACTCAAACCTACCGAGAGCGATCATGGATGGGCGGAAGGAGGACAAAAAACAAGAGTAAGAAGAAGGAAGCAGCCAGA

Alignment

ORF - retro_fcat_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.78 %
• Parental protein coverage: 97.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLLESEQFLTELTRLFQKCRLSGSVFITLKKYDGRTKPIPRK-GSVEGFEPSDNKCLLRATDGKKKIST
          MVLLES..FL..LTR.F.KC.LS.SV.ITLKKYDG.TKPIPRK..S.EG.EPSD.KCLLRATDGK.....
Retrocopy MVLLESNHFLMKLTRFF*KCCLSCSVLITLKKYDGQTKPIPRK<SSAEGCEPSDSKCLLRATDGKG*HCG

Parental  VVSSKEVNKFQMAYSNLLRANMDGLKKRDKKSKSKKSK
          V...K.............R..M.G.....K..K.....
Retrocopy VLPKKRTGFRWLTQTYRERSWMGGRRTKNKSKKKEAAR

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	82.41 RPM
SRP017611_kidney	0.21 RPM	78.32 RPM
SRP017611_liver	0.00 RPM	36.59 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1684 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1684 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 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Felis catus	ENSFCAG00000030207	2 retrocopies	retro_fcat_1425, retro_fcat_1684 ,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Microcebus murinus	ENSMICG00000007637	1 retrocopy	retro_mmur_487,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Pteropus vampyrus	ENSPVAG00000002186	2 retrocopies	retro_pvam_152, retro_pvam_323,
Ictidomys tridecemlineatus	ENSSTOG00000015627	9 retrocopies	retro_itri_1334, retro_itri_1501, retro_itri_1633, retro_itri_382, retro_itri_432, retro_itri_707, retro_itri_710, retro_itri_799, retro_itri_824,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,