RetrogeneDB ID: retro_fcat_946

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:34554332..34554961(+)
• Located in intron of: ENSFCAG00000008541

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000007419
• Aliases: None
• Description: None

Sequence

>retro_fcat_946
GACAATAAAGGGCCAGCAGGAAAATGTACCAAGACTAAGAACCCAGCATGGGCATCAGCTAAAGTGGATAAACTCCAGCC
TTCAGAAGGCTTCAGCCTCTAAAAACTCTGGGGAGAATCTAGCAGTTAGTGGCTGATAAAGTCAGGGCCAGAAAGCTGAC
TAGACAAAGGTGTGGATGTGATGTTCAGCATTGGAGAGCTTTAAGCACAGTCCTAGCAGACAGCGTGCTGGGATGATGTT
ACAACTACCAGGCCCAGAACTTCCTTCCAGTCCTGAAGCTGGAGGAAGAAGCCTTCTACCATAGCAACTGCAAAGAGCCA
GACATCAAAGCACTTGTGAGGCCTGTGAAAGAGGCTGACTCAGACTATACATAGGTTGAAAAAAACAATCCCTGTTATGA
CCCATCCAGCAAAGAAGAGAGCCCCAAATGGTCCAGGGTGGATGTGCAGTTTGTTTGGATGAGGAAGAATTTCAGTATCC
TGGCTGAGCTCAAAACCCATCACCAAGCTCACAAAGCCACTGGACACCCCTTAAAAGAGATGGCTCTCTTCACTCGCCAA
AGACTCAACTCAGCCCTGACCTGAGAGGAGTTTGATTTTATTTTGAGCCTAGAGAAAAAGGAAACAAGT

Alignment

ORF - retro_fcat_946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.16 %
• Parental protein coverage: 92.58 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DNKGPAGKRTKTKNPVGASAQV-VNSSPQKTSASKTCGKNL-SSYWLMKSEAESRLEKGVDVKFSIEDLK
          DNKGPAGK.TKTKNP..ASA.V..NSS.QK.SASK..G.NL.SS.WL.KS..ES.L.KGVDV.FSI..L.
Retrocopy DNKGPAGKCTKTKNPAWASAKV>INSSLQKASASKNSGENL<SS*WLIKSGPES*LDKGVDVMFSIGEL*

Parental  AQPKQTACWDGVR-NYQARNFLRAMKLEQEAFFYHSNCKEPGIAGLVKIVKEAYPDHTQFEKNNPHYDPS
          AQ..QTACWD.V..NYQA.NFL...KLE.EAF.YHSNCKEP.I..LV..VKEA..D.T..EKNNP.YDPS
Retrocopy AQS*QTACWDDVT<NYQAQNFLPVLKLEEEAF-YHSNCKEPDIKALVRPVKEADSDYT*VEKNNPCYDPS

Parental  SKEDNPKWSMVDVQFVRMMKRFITLAELKTHHQAHKATGGPLKNMALFSRQRLSIQPLTQEEFDFILSLE
          SKE..PKWS.VDVQFV.M.K.F..LAELKTHHQAHKATG.PLK.MALF.RQRL....LT.EEFDFILSLE
Retrocopy SKEESPKWSRVDVQFVWMRKNFSILAELKTHHQAHKATGHPLKEMALFTRQRLN-SALT*EEFDFILSLE

Parental  EKEPS
          .KE.S
Retrocopy KKETS

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	0.80 RPM	21.00 RPM
SRP017611_kidney	0.00 RPM	15.66 RPM
SRP017611_liver	0.00 RPM	7.38 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_946 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_946 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007294	1 retrocopy	retro_amel_300,
Canis familiaris	ENSCAFG00000009772	1 retrocopy	retro_cfam_877,
Cavia porcellus	ENSCPOG00000006567	1 retrocopy	retro_cpor_1542,
Felis catus	ENSFCAG00000007419	1 retrocopy	retro_fcat_946 ,
Macropus eugenii	ENSMEUG00000008297	1 retrocopy	retro_meug_287,
Mustela putorius furo	ENSMPUG00000009185	1 retrocopy	retro_mputfur_1114,