RetrogeneDB ID: retro_fcat_1437

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:39992639..39993340(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMYD2
• Ensembl ID: ENSFCAG00000018917
• Aliases: None
• Description: SET and MYND domain containing 2 [Source:HGNC Symbol;Acc:20982]

Sequence

>retro_fcat_1437
GCAATATTTCCTGAGGTTGCACTGATGAATCATAGTTGTTGCCCCACTGTCATTGTGACCTACAAGGGGATCCTGGCAGA
AGTAAGAGCTGTACAGGATATGAACCTGGGAGAGGAGGTTTGTATCAGCTATGTTGACCTCCTGTACCCAACAGAAGTCA
GGAATGACCCGTGAAGAGAGTCTTACTATTTTACCTGTCAGTGCCAGGAGTATACCACCAAAGACAAGGATAAGGCCAAA
TTGAAAATCCAAAAGCTCAGCCATTCCCCCAAAGGCAGAAATAATCTCTGACACGATCAGATATGCACGCAATGTCCTGG
AGGAGTTCTGGGGGGCCAAGCACTACAAATGCCCTCGCGAGCTGCTGAGTATCTGTGAGCTCAGCCAGGAGAAGATGAGC
TCCGTGTTTGAGGACAGCAATGTGTACATATGGCACATGATGTACCCAGCCATGGGTGTCTGCTTGTATGTGCAGGACTG
GGAAGGAGCCCTGTGATATGGACAGGAAATCGTTAAACCCTCCAGCAAGCATTCTCCTCTGTATTCCATGGCTTCCATGT
GGTTGAAGCTGGGAAGGCCATACAGGGGCGGGGAAATAAAGCTGCTGGAGAGAAAGCAGTGAAGAAGACCATTGCAATGA
GGGAAGGAGCTCTGGCAAAGATCATTTGTACATTAATGATATCAAACAAGAAGTTGAAACT

Alignment

ORF - retro_fcat_1437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEINPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCQCQE
          AIFP.VALMNHSCCP.VIVTYKG.LAEVRAVQ..N.GEEV..SY.DLLYPTE.RND..R.SY.FTCQCQE
Retrocopy AIFPEVALMNHSCCPTVIVTYKGILAEVRAVQDMNLGEEVCISYVDLLYPTEVRNDP*RESYYFTCQCQE

Parental  CTTKDKDKAKVEIRKLSD-PPKAETIRDMVRYARNVIEEFRRAKHYKAPPSELLEICELSQEKMSSVFED
          .TTKDKDKAK..I.KLS..PPKAE.I.D..RYARNV.EEF..AKHYK..P.ELL.ICELSQEKMSSVFED
Retrocopy YTTKDKDKAKLKIQKLSH>PPKAEIISDTIRYARNVLEEFWGAKHYKC-PRELLSICELSQEKMSSVFED

Parental  SNVYMLHMMYQAMGVCLYMQDWEGALRYGQKIIKPYSKHYPLYSLNVASMWLKLGRLHMGLE-NKAAGER
          SNVY..HMMY.AMGVCLY.QDWEGAL.YGQ.I.KP.SKH.PLYS...ASMWLKLGR...G.E.NKAAGE.
Retrocopy SNVYIWHMMYPAMGVCLYVQDWEGAL*YGQEIVKPSSKHSPLYSM--ASMWLKLGRPYRGGE<NKAAGEK

Parental  ALKKAIAIMEVA-HGKDHPYISEIKQEIDS
          A.KK.IA..E.A..GKDH.YI..IKQE...
Retrocopy AVKKTIAMREGA<SGKDHLYINDIKQEVET

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	59.57 RPM
SRP017611_kidney	0.00 RPM	13.29 RPM
SRP017611_liver	0.10 RPM	11.63 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1437 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1437 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014059	1 retrocopy	retro_dnov_805,
Felis catus	ENSFCAG00000018917	1 retrocopy	retro_fcat_1437 ,