RetrogeneDB ID: retro_fcat_1028

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:53854249..53854729(-)
• Located in intron of: ENSFCAG00000000247

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN2
• Ensembl ID: ENSFCAG00000029385
• Aliases: None
• Description: tetraspanin 2 [Source:HGNC Symbol;Acc:20659]

Sequence

>retro_fcat_1028
CTGATGGGGTTGGCTGTCTTTGCTTTTGGACTATGATTTTGGTTTGGAGGCACCATGAAGAATTTCTTATCAGAGAAGGG
GTCACCAGAGTAATTCTACATGAGGCTCTATGTGTTGGTTGGAACAGGGGTCCTGATAACAGTTGTGAGCCTCTTCGAGT
GCTAGAAAGCCACGAGACAGTTGCATTGTGTGCTCAGCATTTTTACCTGCCTAGAGGTGATATTTGCTGCTGAAGTAACC
ATTGGGATATTTGTTTTTTATAGGCAAGGGTGTAGCTATAGGACGTGCTCAGACCATGTGTGTGGAGGCTTATAACTATT
ACCTTACAGAGAGTGAAAAAGGAAATAGGGCTGTCAGTACCTTCCACTCAACATTTCAGTGCTTTGAAACAAAAGTTCTG
AAGAGATCCAACCCACAGAGCTGAAAGTGCTTCTAGGACACAAGCAATATATTGATGAGACTGGGACCATAATCAGTGTT

Alignment

ORF - retro_fcat_1028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.96 %
• Parental protein coverage: 80.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAGSAVIGFGLWFRFGGTMKDFSSEDKSPEYFYMGLYVLVGAGALMMAVGFFGCCGAMRESQCVLGSFFT
          L.G.AV..FGL.F.FGGTMK.F.SE..SPE.FYM.LYVLVG.G.L...V..F.C..A.R...CVL.S.FT
Retrocopy LMGLAVFAFGL*FWFGGTMKNFLSEKGSPE*FYMRLYVLVGTGVLITVVSLFEC*KATRQLHCVL-SIFT

Parental  CLLVIFAAEVTTGVFA-FIGKGVAIRHVQTMYEEAYNDYLKDREKGNGTLITFHSTFQCCG-KESSEQVQ
          CL.VIFAAEVT.G.F..FIGKGVAI...QTM..EAYN.YL...EKGN....TFHSTFQC.....SSE..Q
Retrocopy CLEVIFAAEVTIGIFV>FIGKGVAIGRAQTMCVEAYNYYLTESEKGNRAVSTFHSTFQCFE<NKSSEEIQ

Parental  PTCPKELLGHKNCIDEIEAIISI
          PT..K.LLGHK..IDE...IIS.
Retrocopy PTELKVLLGHKQYIDETGTIISV

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	9.18 RPM
SRP017611_kidney	0.00 RPM	9.38 RPM
SRP017611_liver	0.00 RPM	0.40 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1028 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1028 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010910	1 retrocopy	retro_amel_1051,
Canis familiaris	ENSCAFG00000009732	1 retrocopy	retro_cfam_1227,
Felis catus	ENSFCAG00000006863	1 retrocopy	retro_fcat_1098,
Felis catus	ENSFCAG00000029385	1 retrocopy	retro_fcat_1028 ,
Mustela putorius furo	ENSMPUG00000001674	1 retrocopy	retro_mputfur_793,