RetrogeneDB ID: retro_fcat_1962

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:4420444..4420810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000008469
• Aliases: None
• Description: None

Sequence

>retro_fcat_1962
AAGCCTCATGGGAACAGGACTCCTAAAACAACCGATATGTCTAGAAGGCTGTGGTCCAAAGCCATTTTTGCTGGCTATAA
GCGGGGTCTCTGGAACCAGAGGGAGCACACAGCACTTCTTAAAATTGAAGGTGTTTATGCTCAAGATGAAACTGAGTTCT
ATGTAGGCAAGAGATGCGCTTCTGTGTACAAAACAAAGAACAACACAGTGACTCCTGATGGCAATGGAATAAAACCAGAG
TAGTCTGAGGAATAAGTAACTCGTGCTCATGGAAACAGAGGCAAGGTTTGTGCCTAATTCCAAAGCAACCTTCCTTCTAA
AGCCATTGGCCACAGAATCTGTGTGATGCTGTACCCTTCAAGGATT

Alignment

ORF - retro_fcat_1962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.84 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPAGNRTPETTNMSGRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTV
          .P.GNRTP.TT.MS.RLWSKAIFAGYKRGL.NQREHTALLKIEGVYA.DETEFY.GKRCA.VYK.KNNTV
Retrocopy KPHGNRTPKTTDMSRRLWSKAIFAGYKRGLWNQREHTALLKIEGVYAQDETEFYVGKRCASVYKTKNNTV

Parental  TPGGKP-NKTRVIWGK-VTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI
          TP.G...NKTRV..G..VTRAHGN.G.V.A.F.SNLP.KAIGHRI.VMLYPSRI
Retrocopy TPDGNG<NKTRVV*GI>VTRAHGNRGKVCA*FQSNLPSKAIGHRICVMLYPSRI

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	33.05 RPM
SRP017611_kidney	0.00 RPM	153.25 RPM
SRP017611_liver	0.00 RPM	88.15 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1962 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1962 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 1 parental gene, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000008469	36 retrocopies	retro_fcat_1042, retro_fcat_1056, retro_fcat_1074, retro_fcat_1208, retro_fcat_1212, retro_fcat_1238, retro_fcat_1242, retro_fcat_1272, retro_fcat_1303, retro_fcat_1447, retro_fcat_1486, retro_fcat_1494, retro_fcat_150, retro_fcat_1529, retro_fcat_1553, retro_fcat_1589, retro_fcat_1593, retro_fcat_1616, retro_fcat_163, retro_fcat_1633, retro_fcat_1731, retro_fcat_1962 , retro_fcat_199, retro_fcat_209, retro_fcat_217, retro_fcat_250, retro_fcat_294, retro_fcat_346, retro_fcat_347, retro_fcat_408, retro_fcat_535, retro_fcat_608, retro_fcat_621, retro_fcat_679, retro_fcat_764, retro_fcat_813,