RetrogeneDB ID: retro_fcat_317

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:41337732..41338010(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDE6D
• Ensembl ID: ENSFCAG00000002232
• Aliases: None
• Description: phosphodiesterase 6D, cGMP-specific, rod, delta [Source:HGNC Symbol;Acc:8788]

Sequence

>retro_fcat_317
CTAGATTGGATATACTTCTGGGATGCTGAGACATGGAAAACACTCTGGCCAGGAGCAGAAGACCTGCCAGTCCCTGAAGT
GGAGAATGAAGCCCCTGTTCTCAAGAAAACCCTCAAGCTCAAGGCAGTGTGTCCAGAAGTGACATTGTCTTCAGCAGAGC
AAATGGAAAATTCTTTCTGGAACAAAAAGTTTACTTCAAAGGAAAATGCCTAGAAAAACGGATCTTCAAATTTGGCTTTG
TGGTCCCTAACTCCACAATAACCTGGCAGTCCCAGATT

Alignment

ORF - retro_fcat_317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.02 %
• Parental protein coverage: 62. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSAEQME-KFRLEQKVYFKGQ
          L.W....DAET.K.LW.G.EDL.VP.VE.EA.V.KK.LK.KAV..E...SSAEQME.KF.LEQKVYFKG.
Retrocopy LDWIYFWDAETWKTLWPGAEDLPVPEVENEAPVLKKTLKLKAVCPEVTLSSAEQME<KFFLEQKVYFKGK

Parental  CLEEWFFEFGFVIPNSTNTWQSLI
          CLE...F.FGFV.PNST.TWQS.I
Retrocopy CLEKRIFKFGFVVPNSTITWQSQI

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	14.00 RPM
SRP017611_kidney	0.00 RPM	10.00 RPM
SRP017611_liver	0.00 RPM	4.65 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_317 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_317 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012101	1 retrocopy	retro_acar_157,
Dasypus novemcinctus	ENSDNOG00000000568	1 retrocopy	retro_dnov_2585,
Felis catus	ENSFCAG00000002232	1 retrocopy	retro_fcat_317 ,
Macropus eugenii	ENSMEUG00000006427	1 retrocopy	retro_meug_1355,
Oryctolagus cuniculus	ENSOCUG00000010403	1 retrocopy	retro_ocun_182,
Pteropus vampyrus	ENSPVAG00000004743	1 retrocopy	retro_pvam_544,
Tursiops truncatus	ENSTTRG00000009165	1 retrocopy	retro_ttru_82,