RetrogeneDB ID: retro_fcat_890

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B3:36767182..36767711(-)
• Located in intron of: ENSFCAG00000025525

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBCH
• Ensembl ID: ENSFCAG00000003341
• Aliases: None
• Description: 3-hydroxyisobutyryl-CoA hydrolase [Source:HGNC Symbol;Acc:4908]

Sequence

>retro_fcat_890
GCCGGAAATAGCAATTTAATAGCGATTAACCAGTTGCTGTTTGGACTATTCCCTGATGTGGGTGGAGGTTATTTCTTGCC
ATGACTTCAAGGAAAACTTGGTTACTTCCTTGCATTAACAGGATTCGGGCTGAAGGGAAGAGATACATACACCGCAGGAA
TTGCGACACACTTTGTGGATTCTGAAAAGTTGGCATGTTAGAAGATTTGTTAGCCCTAAAATCTCCTTCAAAAGAAAATA
TTGCAGATGTCTTAGAGGTTACCATACAAAGTCCAAGACTGATCAAGACAAGTCTTTTATACTTGAGGACCACATGGACA
AAATAAACAGTTGGTTCTTGGCCAATAGTGTGGAACAGGTTATTGAAAATTTACAGCAAGATAGTCCATCTTTTGCCTTA
GAACAGTTGAAGGTAATTAATAAAATGTCTCCAGCATCCCTAAATATCACACTAAGGCAACTCATGGAGGGGTCTTCAAA
GACCTTGCAAGAAGTATTAACTCTGGAATATCAGTTGAGTCAAGCTTGT

Alignment

ORF - retro_fcat_890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.67 %
• Parental protein coverage: 52.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATEKSLFAMPETAIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVYAAGIATHFVDSEKL-GMLEE
          A....L.A......GLFPDVGGGYFLP.LQGKLGYFLALTGF.LKGRD.Y.AGIATHFVDSEKL.GMLE.
Retrocopy AGNSNLIAINQLLFGLFPDVGGGYFLP*LQGKLGYFLALTGFGLKGRDTYTAGIATHFVDSEKL<GMLE-

Parental  DLIALKSPSKENIADVLEA-YHTKSKIDQDKSFILEEHMDKINSCFSANTVEQIIENLQQDGSSFALEQL
          DL.ALKSPSKENIADVLE..YHTKSK.DQDKSFILE.HMDKINS.F.AN.VEQ.IENLQQD..SFALEQL
Retrocopy DLLALKSPSKENIADVLEV<YHTKSKTDQDKSFILEDHMDKINSWFLANSVEQVIENLQQDSPSFALEQL

Parental  KVINKMSPTSLKITLRQLMEGSSKTLQEVLIMEYRLSQAC
          KVINKMSP.SL.ITLRQLMEGSSKTLQEVL..EY.LSQAC
Retrocopy KVINKMSPASLNITLRQLMEGSSKTLQEVLTLEYQLSQAC

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	12.97 RPM
SRP017611_kidney	0.10 RPM	35.86 RPM
SRP017611_liver	0.40 RPM	75.72 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_890 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_890 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000003341	1 retrocopy	retro_fcat_890 ,
Homo sapiens	ENSG00000198130	1 retrocopy	retro_hsap_3285,
Gorilla gorilla	ENSGGOG00000004988	1 retrocopy	retro_ggor_1317,
Macaca mulatta	ENSMMUG00000007283	1 retrocopy	retro_mmul_2062,
Mus musculus	ENSMUSG00000041426	1 retrocopy	retro_mmus_294,
Nomascus leucogenys	ENSNLEG00000006646	1 retrocopy	retro_nleu_1351,
Pongo abelii	ENSPPYG00000013021	2 retrocopies	retro_pabe_2714, retro_pabe_2827,
Pan troglodytes	ENSPTRG00000012741	1 retrocopy	retro_ptro_2222,
Tupaia belangeri	ENSTBEG00000004132	1 retrocopy	retro_tbel_3398,