RetrogeneDB ID: retro_fcat_647

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:121786550..121787425(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000022091
• Aliases: None
• Description: None

Sequence

>retro_fcat_647
GATGACTCCTTCAACATCTTCTTCAGTGAGGTGGGTGCTGGCAAGTGTGTGCGCAAGGTAGTGTTTATAGACCTGGAACC
CACAGTCATTGGTGACGTTTACACTGGTACCTACTGCCAGCTATTCCACCCTGGGCAGCTCATCACAGGCAAGGAAAATG
CTGCCAATAACCATGCCCAAGGGCAATATACCACTGGCAAGGAGATCATTGACCTTATCTTGGACTAAATTCAGAAAGTG
GCCAACAAGCACACAGGTGTTCAAGACATCTTGGTTTTCCACGGCTTTGGAGGGGGAACTGGTTCTGCTTTCACCTCCCT
GCTAATGGAATAACTATTGATTATGGCAAGAAGTCCAAGCTAGAGTTCTCCATTTACCCAATCCACCAGGTTTCCACAGC
TGTAGTTGAGCCCTGTAACTCCTATTCACTACCCATGTCACCCTGGAGCACTCTGATTGTGCCTTCATGATAGACAAGAG
ACCATCTATGACATCTGTCATAGAAATATCGATATTGAGTGCCCAAACTACACTAATCTTAATTGCTTCATTAGCCGGAT
TGTGTCTTCCGTCACTGCTTTCCTCAGATTTGATGGAGCCCTCAATCTGACAGAATTCCAGACCCGCCTGGTATCCTATC
CCCACATCCATTTCCCTCTGGCCATATATGCCCTTGTCATCTCTACTGAGAAAACCTACCATGAACAGTCCTCTGAGCAG
AGACCACTAGTATGTGAGTTGAGCCAGAAAGCCAGATGGTGAAATGTGACCCTCACCATGGTAAATACATGGCTTGCTGC
CTGTTGTACCATGGCGATGTGGTTCCCAAAGACGTCAGTGCTGCCATTGCCACCAACAAGACCAAGCATCCCCTT

Alignment

ORF - retro_fcat_647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.56 %
• Parental protein coverage: 65.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DDSFNTFFSETGAGKHVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGREIV
          DDSFN.FFSE.GAGK.V...VF.DLEPTV...V.TGTY.QLFHP.QLITGKE.AANN.A.G.YT.G.EI.
Retrocopy DDSFNIFFSEVGAGKCVRKVVFIDLEPTVIGDVYTGTYCQLFHPGQLITGKENAANNHAQGQYTTGKEII

Parental  DLVLDRIRKLADLCTGLQGFLIFHSFGGTGSGFASLLMER-LSVDYGK-SKLEFAIYPAPQVSTAVVEPY
          DL.LD.I.K.A...TG.Q..L.FH.FGG........L.......DYGK.SKLEF.IYP..QVSTAVVEP.
Retrocopy DLILD*IQKVANKHTGVQDILVFHGFGGGTGSAFTSLLME<ITIDYGKKSKLEFSIYPIHQVSTAVVEPC

Parental  NS-ILTTHTTLEHSDCAFMVDN-EAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLT
          NS...TTH.TLEHSDCAFM.D..E.IYDIC.RN.DIE.P.YTNLN..I..IVSS.TA.LRFDGALN..LT
Retrocopy NS<LFTTHVTLEHSDCAFMIDK<ETIYDICHRNIDIECPNYTNLNCFISRIVSSVTAFLRFDGALN--LT

Parental  EFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSV-AEITNACFEP-AQMVKCDPRHGKYMACCMLYRGD
          EFQT.LV.YP.IHFPLA.YA.VIS.EK.YHEQ.S..AE.T....EP..QMVKCDP.HGKYMACC.LY.GD
Retrocopy EFQTRLVSYPHIHFPLAIYALVISTEKTYHEQSSE<AETTSM*VEPESQMVKCDPHHGKYMACCLLYHGD

Parental  VVPKDVNAAIATIKTKRTI
          VVPKDV.AAIAT.KTK...
Retrocopy VVPKDVSAAIATNKTKHPL

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	0.00 RPM
SRP017611_kidney	0.10 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_647 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_647 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011042	2 retrocopies	retro_amel_488, retro_amel_518,
Equus caballus	ENSECAG00000014403	1 retrocopy	retro_ecab_318,
Felis catus	ENSFCAG00000022091	2 retrocopies	retro_fcat_1375, retro_fcat_647 ,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356,