RetrogeneDB ID: retro_fcat_224

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:38001762..38002426(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM147
• Ensembl ID: ENSFCAG00000006373
• Aliases: None
• Description: transmembrane protein 147 [Source:HGNC Symbol;Acc:30414]

Sequence

>retro_fcat_224
CTTGTTCAGTTCAGGAACTGCTTCACCCTGGCCTACTTCCCCTACTTCCTCACTTACAAGTACAGCAGGCTGTCCGAGTA
CAACACCTCCTGAAAGTGTGTGCAGCCTGGGGTCACCCACCTCCTCATGCAGCTTTGCAAGATGGTGTTCCTGGCTACGT
TTTGTTCCCACCTAGGAAGGTGGCATCTATGACTTTATTGGGGAGTTGACCAAGGCCAGTGTGGATGTGACAGACCTGAT
AGACCTAAACCTTGAGATGTCACAGAATGCAGGCAAGGGGGAATACAAGATCACGGTTGCTGCCCCAGGCTAGACCATCT
CCAAGCCCATTATGTCCCACTGCGCTCCCTTCTGGGTTGGAGCCCCGGGCTTTGAGTTTGGCTGGAAATATATCCATATG
AGCACTGACTCCAAAATCAGTTTGGCCCACTACATCGTCGCATCTGCCCAGGTCTGGATGATAACACGCTATGACCTATA
CCACAGTTTTCTGTGAGCAGTGCTCCTACAGATGTTCCTTAGTGTCTATAAGGGCTTTGTCATGGAGACCTTTGTCCACC
TCTGTTCCCTGGACAGCTGGACAGCACTGCTACCTGGAGCAGTGGTAAAAGGGCTGCTAGCCCTCAGCACACTGGTCTTC
GAGGTTACTGTTGTCAACAGGCAT

Alignment

ORF - retro_fcat_224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.77 %
• Parental protein coverage: 98.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFHFGNCFALAYFPYFITYKCSGLSEYNAFWKCVQAGVTYLFVQLCKMLFLATF-FPTWEGGIYDFIGEF
          L..F.NCF.LAYFPYF.TYK.S.LSEYN...KCVQ.GVT.L..QLCKM.FLATF..PT.EGGIYDFIGE.
Retrocopy LVQFRNCFTLAYFPYFLTYKYSRLSEYNTS*KCVQPGVTHLLMQLCKMVFLATF>VPT*EGGIYDFIGEL

Parental  MKASVDVADLIGLNLVMSRNAGKGEYKIMVAALGWATAELIMSRCIPLWVGARGIEFDWKYIQMSIDSNI
          .KASVDV.DLI.LNL.MS.NAGKGEYKI.VAA.G......IMS.C.P.WVGA.G.EF.WKYI.MS.DS.I
Retrocopy TKASVDVTDLIDLNLEMSQNAGKGEYKITVAAPG*TISKPIMSHCAPFWVGAPGFEFGWKYIHMSTDSKI

Parental  SLVHYIVASAQVWMITRYDLYHTFRPAVLLLMFLSVYKAFVMETFVHLCSLGSWTALLARAVVTGLLALS
          SL.HYIVASAQVWMITRYDLYH.F..AVLL.MFLSVYK.FVMETFVHLCSL.SWTALL..AVV.GLLALS
Retrocopy SLAHYIVASAQVWMITRYDLYHSFL*AVLLQMFLSVYKGFVMETFVHLCSLDSWTALLPGAVVKGLLALS

Parental  TLALYVAVVNVH
          TL...V.VVN.H
Retrocopy TLVFEVTVVNRH

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	34.20 RPM
SRP017611_kidney	0.00 RPM	84.20 RPM
SRP017611_liver	0.00 RPM	27.40 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_224 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_224 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010132	1 retrocopy	retro_acar_105,
Ailuropoda melanoleuca	ENSAMEG00000000375	1 retrocopy	retro_amel_1193,
Bos taurus	ENSBTAG00000015920	1 retrocopy	retro_btau_1546,
Canis familiaris	ENSCAFG00000006960	2 retrocopies	retro_cfam_1070, retro_cfam_1265,
Dasypus novemcinctus	ENSDNOG00000004059	1 retrocopy	retro_dnov_1123,
Felis catus	ENSFCAG00000006373	2 retrocopies	retro_fcat_1489, retro_fcat_224 ,
Myotis lucifugus	ENSMLUG00000016383	1 retrocopy	retro_mluc_1889,
Mustela putorius furo	ENSMPUG00000006709	1 retrocopy	retro_mputfur_588,
Tarsius syrichta	ENSTSYG00000008207	1 retrocopy	retro_tsyr_56,
Tursiops truncatus	ENSTTRG00000015114	2 retrocopies	retro_ttru_1406, retro_ttru_219,