RetrogeneDB ID: retro_fcat_1387

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:6047808..6048221(+)
• Located in intron of: ENSFCAG00000003524

Retrocopy information

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

Parental gene information

• Parental gene symbol: OIP5
• Ensembl ID: ENSFCAG00000030520
• Aliases: None
• Description: Opa interacting protein 5 [Source:HGNC Symbol;Acc:20300]

Sequence

>retro_fcat_1387
CACCTGGCCAGAGACCTGCTGCAGCGGGCGGGGCTGGGCGCTTCTCTAGACTCACAAATATGGTGGTATGGGAAGCTCCC
TTTCTAGCTGGCCTTGAAGGTCTCCTCAAAGGCAGCACCAACAACCTCAGATTCTGGACTTCCTGTGGGATTCCCACTGG
TTTCCATTTGTATTCTACCCATGCTGCCCTGGATGCCTTGAGAGGTCACTTCTGCCTTTCCAGTGGCAAAACGCTATGCT
ACCTCTTAAAAACAAAAGCCACAGTAAATGCATCTCAGCTGGGTATTGACAACCTCTCTCTACCAGAAAAGGATGCAGAG
CTGTAAGAGAAGATAACGTGAGTGCATACTTGCCTCAGTTCACTGATGAAGATTCTGAAGGAAGTGACTCCTGACCAGCC
CAAGCCAGAAAAC

Alignment

ORF - retro_fcat_1387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.38 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HLAWDLSPSLGTVV-FSRVTNNVVLETPFLVGIEGSLKGSIYNLLFCTSCGIPIGFHLYSTHAALAALRG
          HLA.DL....G....FSR.TN.VV.E.PFL.G.EG.LKGS..NL.F.TSCGIP.GFHLYSTHAAL.ALRG
Retrocopy HLARDLLQRAGLGA<FSRLTNMVVWEAPFLAGLEGLLKGSTNNLRFWTSCGIPTGFHLYSTHAALDALRG

Parental  HFCLSSDKMICYLLKTKAIVNASEMDIHNLSLPEKIAELKEKIMLTHTHLNSLMKILKEVTPDQPKPEN
          HFCLSS.K..CYLLKTKA.VNAS...I.NLSLPEK.AEL.EKI...HT.L.SLMKILKEVTPDQPKPEN
Retrocopy HFCLSSGKTLCYLLKTKATVNASQLGIDNLSLPEKDAEL*EKIT*VHTCLSSLMKILKEVTPDQPKPEN

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	0.11 RPM	0.92 RPM
SRP017611_kidney	0.00 RPM	0.31 RPM
SRP017611_liver	0.00 RPM	0.20 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1387 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1387 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016777	1 retrocopy	retro_amel_242,
Bos taurus	ENSBTAG00000010766	1 retrocopy	retro_btau_1700,
Felis catus	ENSFCAG00000030520	1 retrocopy	retro_fcat_1387 ,
Myotis lucifugus	ENSMLUG00000009765	2 retrocopies	retro_mluc_2106, retro_mluc_2341,
Mustela putorius furo	ENSMPUG00000008828	2 retrocopies	retro_mputfur_1518, retro_mputfur_1534,
Otolemur garnettii	ENSOGAG00000033746	1 retrocopy	retro_ogar_1761,
Sorex araneus	ENSSARG00000009593	2 retrocopies	retro_sara_351, retro_sara_629,