RetrogeneDB ID: retro_fcat_1730

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E3:23890200..23890886(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAG1
• Ensembl ID: ENSFCAG00000000091
• Aliases: None
• Description: protein kinase, AMP-activated, gamma 1 non-catalytic subunit [Source:HGNC Symbol;Acc:9385]

Sequence

>retro_fcat_1730
ACAGTATTGGTATAGATCTATGAGCTGAAAGAGCACAAAATAGAAACTTGGAGGGAGGTGTAGGTACGGGACTCCTCGAA
TCCCTTGTCCGCATTGCTTCTAATGCCAGCTTATTTGATGATGTCTCTTCATTAATTCAAAATAAGATCCGCAGGCTGCC
AGTTATTGACTCAGAATCAGGCAACACCTTGTACATATTCACCTATAAGCACGTTCTCAAATGTCTCAAATTGTTTGCTG
ATGAATTCCCCAAGCCAGAGTTCGTGTCTAACTCTCTGGAAAGAACTTCAAGTTAGCACTTAGGCCAATGCTGCTATGGC
CCACACCACCACCCCTGTCTACATGCCTCTGGGCATTTTGTACAATGCGGATTCTCAGCCCTGCCACTGGTGGATGAGAA
AGAGTGTGTGGTGAACTTCTACCCCAAGTTTTATGTTATCAGTGTAGCAGCAGAACAAACTTAGAGTAACCTGGATGTGT
CAGTGACCAAAGCCCTACAATGTTGATCACGTTACTTCAGATGTGTCTCCAAGTGCTACCTGCATGAGACTCCGGAGACC
ATCATCAACAGGCTGGTGGATGCAGAGATTCACCTCTTTGTAGTGGTGGATGGGAACGATGCAGTCAAGGAAACCGTATC
ACTGTCTGACATCCCTCAGGTCTCGGTGCTCACTGGCAGGGACAGA

Alignment

ORF - retro_fcat_1730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.97 %
• Parental protein coverage: 69.82 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SALVQIYELEEHKIETWREVYLQDSFKPL-VCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTH
          ..LV.IYEL.EHKIETWREV...DS..PL.V.I..NASLFD.VSSLI.NKI.RLPVID.ESGNTLYI.T.
Retrocopy TVLV*IYELKEHKIETWREV*VRDSSNPL<VRIASNASLFDDVSSLIQNKIRRLPVIDSESGNTLYIFTY

Parental  KRILKFLKLFITEFPKPEFMSKSLE-ELQIGTYANIAMVRTTTPVYVALGI-FVQHRVSALPVVDEKGRV
          K..LK.LKLF..EFPKPEF.S.SLE.ELQ..T.AN.AM..TTTPVY..LGI.FVQ...SALP.VDEK..V
Retrocopy KHVLKCLKLFADEFPKPEFVSNSLE>ELQVST*ANAAMAHTTTPVYMPLGI<FVQCGFSALPLVDEKECV

Parental  VDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRLVEAEVHRLVVVDEND
          V..Y.KF.VI..AAE.T..NLDVSVTKALQ..S.YF..V.KCYLHET.ETIINRLV.AE.H..VVVD.ND
Retrocopy VNFYPKFYVISVAAEQT*SNLDVSVTKALQC*SRYFRCVSKCYLHETPETIINRLVDAEIHLFVVVDGND

Parental  VVKGIVSLSDILQALVLTGGEK
          .VK..VSLSDI.Q..VLTG...
Retrocopy AVKETVSLSDIPQVSVLTGRDR

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	48.20 RPM
SRP017611_kidney	0.00 RPM	33.70 RPM
SRP017611_liver	0.00 RPM	20.12 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1730 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1730 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006964	2 retrocopies	retro_amel_1722, retro_amel_406,
Choloepus hoffmanni	ENSCHOG00000006397	1 retrocopy	retro_chof_32,
Callithrix jacchus	ENSCJAG00000020827	2 retrocopies	retro_cjac_3045, retro_cjac_3892,
Felis catus	ENSFCAG00000000091	1 retrocopy	retro_fcat_1730 ,
Felis catus	ENSFCAG00000003842	2 retrocopies	retro_fcat_237, retro_fcat_240,
Myotis lucifugus	ENSMLUG00000011156	2 retrocopies	retro_mluc_2417, retro_mluc_451,
Oryctolagus cuniculus	ENSOCUG00000008409	1 retrocopy	retro_ocun_829,
Sus scrofa	ENSSSCG00000000185	1 retrocopy	retro_sscr_210,
Tursiops truncatus	ENSTTRG00000004730	1 retrocopy	retro_ttru_497,