RetrogeneDB ID: retro_fcat_1267

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:50196099..50197030(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPKOW
• Ensembl ID: ENSFCAG00000003818
• Aliases: None
• Description: G patch domain and KOW motifs [Source:HGNC Symbol;Acc:30677]

Sequence

>retro_fcat_1267
ATGGCGGAGGCTGAAGAGGGTACTTTGTGGCCCACAGGAGCCTCTGCTGCCTCAATTAAATTCAGCTTTAGTCGCACAAT
GGAGCAGAGACTGCTGGCGGATACAGATGACTCAGGTGTGGCTCTGGAGGAGAAGGATTTCTTAAAGACCCTGGAAGGGA
GCAAGCTTCTGAGAATGAAACCCTCAGAACCCCCCAAGGAACTCGTCATCCTTTTGATCCAGAATGGCCATTGCAGGCAG
CTACCGACCCAGTCTCTGGGTCATCCACAAATACTGAGGCCTTGGTGGATATGGTGCTGTCCCAGGCTGTGAAGGAGCTC
ACTGAGAACTCCAAGAAGTCCCTGGAGGAGAGAGAAAAATCAGCAAGCCCCATGTCAACCCCATGCTTGCTAACCCCATG
ATCCAGCAAGAATGCATCCCCAACCAGGAGGTGGCAGATAGCAAACCCTGGGCTGAGACAGTGCTGGAGGAAGCTGACTA
GGAGGCAGTCCCTATAGAAGCCTATGGGCTGGCTGTGTTATGAGGTATGGGCTGGAAACCTGGCGAGGGCGTTGGCCGCA
CCTTCAATCAAGTGTTGAAGCCCCGTGTTAACCCACCAAGGCCAAAGGGGTTAGGCCTGGGTGCGAACCTGACTGAAGTC
GGGGTCCTGGCCCCCCACCGGCCTCCACCCGAAGCCCAGATGAGGAGCAAGAGAAGGATAAGGAAGACCAGCCTCAAGGA
CTGGTGCCCCAGGGAGCTGTGGTAGTTCTTTCTGGCCCTCACCAAGGCCTCTATGGAAAGTAGAAGGCCTCGATCCTGAC
AGCGTTCGGGCCATGGTTCACCTGGCCATGGGGAGCTGAATGGTAACTGTTAGTGAATACTGGCTGCGCCTGTCTCCCAG
CAGGAGTTTGACAAGAACTCCTTGGATCTCAGCCAGTTGCATAAAACCTCC

Alignment

ORF - retro_fcat_1267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 65.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MADAEDGTLRPAGASAAPISFSFSRTSARRRLADPGDDASAAPEEKDFLKTVEGRELQSVKPSETPKELV
          MA.AE.GTL.P.GASAA.I.FSFSRT...R.LAD..DD...A.EEKDFLKT.EG..L...KPSE.PKELV
Retrocopy MAEAEEGTLWPTGASAASIKFSFSRTMEQRLLADT-DDSGVALEEKDFLKTLEGSKLLRMKPSEPPKELV

Parental  IPLIQNGHRRQPPTQA-PGPSTNTEALVEGVLSQAVKEIIEDSKKSLEERENSG---IDPMLAIP-MIQK
          I.LIQNGH.RQ.PTQ...G.STNTEALV..VLSQAVKE..E.SKKSLEERE.S......P.L..P.MIQ.
Retrocopy ILLIQNGHCRQLPTQS<SGSSTNTEALVDMVLSQAVKELTENSKKSLEEREKSASPMSTPCLLTP<MIQQ

Parental  GCIPNGEGADSEPRAETVPEEADYEAVPVEAYGLAMLRGMGWKPGEGIGRTFNQVVKPRVNSLRPKGLGL
          .CIPN.E.ADS.P.AETV.EEAD.EAVP.EAYGLA.L.GMGWKPGEG.GRTFNQV.KPRVN..RPKGLGL
Retrocopy ECIPNQEVADSKPWAETVLEEAD*EAVPIEAYGLAVL*GMGWKPGEGVGRTFNQVLKPRVNPPRPKGLGL

Parental  GANLTEVQALA-PTGPHRLPKP-DEEQEKDKEDQPQGLVPGGAVVVLSGPHRGLYG-KVEGLDPDNVRAM
          GANLTEV..LA.PTG.H..PKP.DEEQEKDKEDQPQGLVP.GAVVVLSGPH.GLYG.KVEGLDPD.VRAM
Retrocopy GANLTEVGVLA>PTGLH--PKP>DEEQEKDKEDQPQGLVPQGAVVVLSGPHQGLYG<KVEGLDPDSVRAM

Parental  VRLAVGSRMVTVSEYYLQ-PVSQQEFDKNSLDLMQQNGTA
          V.LA.GS.MVTVSEY.L..PVSQQEFDKNSLDL.Q...T.
Retrocopy VHLAMGS*MVTVSEYWLR<PVSQQEFDKNSLDLSQLHKTS

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	11.25 RPM
SRP017611_kidney	0.00 RPM	13.50 RPM
SRP017611_liver	0.00 RPM	6.77 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1267 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1267 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013270	2 retrocopies	retro_cpor_148, retro_cpor_725,
Felis catus	ENSFCAG00000003818	1 retrocopy	retro_fcat_1267 ,
Mus musculus	ENSMUSG00000031148	1 retrocopy	retro_mmus_3156,