RetrogeneDB ID: retro_fcat_1133

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:148598639..148599157(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000007803
• Aliases: None
• Description: None

Sequence

>retro_fcat_1133
TTTTCTGCGTTCCTAGTCCCCATCTTCTTCCTGGAGCTGAAAACAGGGGTCCTAGCCTTCGTTTTCAAGGACTGGATTCA
AGACCAGCTCGATTTCCTCGTAAACAAAAACATCAAGGCCTATCGGGACAACACTGATCTCCAGAACCTCATTTACTTTG
CTCAGGAATATTGGTCTTGCTGTAGAGCACGAGGGCCTAATGACTGGAACCTCAATATCTATTTCAACTGCACCGACTTG
AACCCCAGCCAGGAGCGCTGCGAGGTGCCCTTCTCCTGCTGCATCAGGGACTCTGCGGAACATGTCCTCAACGTACAGTG
TGACTAGGATGTACTGCTCAGACTGGAGCTGGAGCAGCAGAGCTCCGTCCATACCAAAGGCTGCATCGGCCAATTTGAGA
AGCGGCCACAGAACAACCTGATCGTCGTGGCTGGGCTCTTTGTGAGCATCGCCCTCCTCCAGATCTTTGGTCTGGCCCAG
AGCCTTGTGAGTGACATCAGGCAGTGGAGGCCAACTGG

Alignment

ORF - retro_fcat_1133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.84 %
• Parental protein coverage: 58.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FSVFLGLIFFLELATGILAFVFKDWIRDQLNFFINNNVKAYRDDIDLQNLIDFAQEYWSCCGARGPNDWN
          FS.FL..IFFLEL.TG.LAFVFKDWI.DQL.F..N.N.KAYRD..DLQNLI.FAQEYWSCC.ARGPNDWN
Retrocopy FSAFLVPIFFLELKTGVLAFVFKDWIQDQLDFLVNKNIKAYRDNTDLQNLIYFAQEYWSCCRARGPNDWN

Parental  LNIYFNCTDLNPSRERCGVPFSCCVRDPAEDVLNTQCGYDVRLKLELEQQGSIHTKGCVGQFEKWLQDNL
          LNIYFNCTDLNPS.ERC.VPFSCC.RD.AE.VLN.QC..DV.L.LELEQQ.S.HTKGC.GQFEK..Q.NL
Retrocopy LNIYFNCTDLNPSQERCEVPFSCCIRDSAEHVLNVQCD*DVLLRLELEQQSSVHTKGCIGQFEKRPQNNL

Parental  IVVAGVFVGIALLQIFGICLAQNLVSDIK-AVKANW
          IVVAG.FV.IALLQIFG..LAQ.LVSDI..AV.ANW
Retrocopy IVVAGLFVSIALLQIFG--LAQSLVSDIR<AVEANW

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	24.45 RPM
SRP017611_kidney	0.00 RPM	7.94 RPM
SRP017611_liver	0.00 RPM	6.37 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1133 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1133 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007218	2 retrocopies	retro_amel_1365, retro_amel_979,
Canis familiaris	ENSCAFG00000016638	2 retrocopies	retro_cfam_1585, retro_cfam_704,
Callithrix jacchus	ENSCJAG00000007278	1 retrocopy	retro_cjac_2289,
Equus caballus	ENSECAG00000022322	1 retrocopy	retro_ecab_554,
Felis catus	ENSFCAG00000007803	1 retrocopy	retro_fcat_1133 ,
Mustela putorius furo	ENSMPUG00000012505	1 retrocopy	retro_mputfur_428,