RetrogeneDB ID: retro_fcat_1441

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:54013557..54014155(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSFCAG00000012596
• Aliases: None
• Description: tropomyosin 3 [Source:HGNC Symbol;Acc:12012]

Sequence

>retro_fcat_1441
GCTGAGGCTGAGGTGGCATCCTTGACCCCTAGGATGCAGCTGGTTGATGAGGAGCTGAACAGTGCCCAGGAGCACCTGGC
AGCTGCCCTGCAAAAGTGGAGGAAACTGAGAAAGCTGCTACTCAGAGCAAGAGAGGTATGGACGTTATTGAAAACCTAGC
CTTAACATATGAAGAAAAGATGGAACTCCAGGAAATCAACTCTAAGAAGCTTAGCACATTGCAGAAGAGGCAAATCTAAA
GTCCAAAAAGGGGGCTCAGAAGTTGGTGATTATTGAGGAGCACGAGGAATGACCTGAGCTGGCATAGTCTCGTTGCCAAG
ACATGGATGAGCAGATCAGACTGATGGACCAGAACCTGAAGTGCCTGAGAGCTACTGCAGAAAATTACTCTCAAGCAGAG
GACACATATGAAGAGGAGATAAATATTCTTACAGATAAACTCAAGGAAGCAGAGACCCGTGCACGATGAGTTTGCTGACA
GGTCAGTGGCCAAACTGGAGAAGACAACTGATGACCTGGGACATAGCTGAAATGCGCCAAAGAGGAACACCTCTGTACAC
AAAGGATGCTGGACCAGATTCCGCTTGACCTGAATGAG

Alignment

ORF - retro_fcat_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.98 %
• Parental protein coverage: 71.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AEAEVASLNRRIQLVEEELDRAQERLATALQK-LEEAEKAADESERGMKVIENRALKDEEKMELQEI-QL
          AEAEVASL..R.QLV.EEL..AQE.LA.ALQK..EE.EKAA..S.RGM.VIEN.AL..EEKMELQEI.QL
Retrocopy AEAEVASLTPRMQLVDEELNSAQEHLAAALQK<VEETEKAATQSKRGMDVIENLALTYEEKMELQEI<QL

Parental  KEAKHIAEEADRKYEEVARKLVIIEGDLERTEERAELAESRCREMDEQIRLMDQSLKCLSA-AEEKYSQK
          .EA.HIAEEA..K....A.KLVI.....E..EE..ELA.SRC..MDEQIRLMDQ.LKCL.A.AE......
Retrocopy *EA*HIAEEANLKSKKGAQKLVI----IEEHEE*PELA*SRCQDMDEQIRLMDQNLKCLRATAENYSQAE

Parental  EDKYEEE-IKILTDKLKEAETRAEFAERSVAKLEKTIDDLEDK-LKCTKEEHLCTQRMLDQTLLDLNE
          ....EE..I.......K......EFA.RSVAKLEKT.DDL....LKC.KEEHLCTQRMLDQ..LDLNE
Retrocopy DTYEEEI>IFLQINSRKQRPVHDEFADRSVAKLEKTTDDLGHS<LKCAKEEHLCTQRMLDQIPLDLNE

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	51.19 RPM
SRP017611_kidney	0.00 RPM	32.36 RPM
SRP017611_liver	0.00 RPM	29.92 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1441 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1441 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 13 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441 ,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,