RetrogeneDB ID: retro_fcat_1312

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:151334683..151335000(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMIM19
• Ensembl ID: ENSFCAG00000031243
• Aliases: SMIM19, CB1H8orf40
• Description: small integral membrane protein 19 [Source:HGNC Symbol;Acc:25166]

Sequence

>retro_fcat_1312
CCTAGAGGTTAGGGGGTGATGGATGCCAATGGCTCTATCCATTATGGCCTTCACAAGGCCTAGAATGAAGCCACCAACTT
TTACTGGGTCAGGGTCCTTATCGGCTTTGGGCTCTTAATGTGGGTCAAGAGGAATAAAAGGAAATTATGAGAATATTCAG
TGTGCCGCCTACAGCAGAAACTTGGTCAGAGCCCAACTTTTATGACACGATAAGCCAAATTCGTTTAAGATAGCAACTGG
AAATGTATTCCATTTCCAGGCAGTCTGACTATCAGCAGCTACAAAACCAAGCTAACACTATGCAGCTCTCATTGGAA

Alignment

ORF - retro_fcat_1312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGGYGVMGDDGSMDYSVHEAWNEATNVYLVVILVSFVLFMYAKRNKRK-IMRIFSVPPTAETLSEPSFYD
          P.G.GVM...GS..Y..H.A.NEATN.Y.V..L..F.L.M..KRNKRK.IMRIFSVPPTAET.SEP.FYD
Retrocopy PRG*GVMDANGSIHYGLHKA*NEATNFYWVRVLIGFGLLMWVKRNKRK<IMRIFSVPPTAETWSEPNFYD

Parental  TISKIRLRQQLEMYSISRKYDYQQPQNQADSVQLSLE
          TIS.IRLR.QLEMYSISR..DYQQ.QNQA...QLSLE
Retrocopy TISQIRLR*QLEMYSISRQSDYQQLQNQANTMQLSLE

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	24.10 RPM
SRP017611_kidney	0.00 RPM	37.00 RPM
SRP017611_liver	0.00 RPM	55.20 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1312 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1312 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005067	1 retrocopy	retro_amel_346,
Cavia porcellus	ENSCPOG00000002665	1 retrocopy	retro_cpor_1019,
Felis catus	ENSFCAG00000031243	1 retrocopy	retro_fcat_1312 ,
Pteropus vampyrus	ENSPVAG00000014829	1 retrocopy	retro_pvam_282,
Sorex araneus	ENSSARG00000008851	2 retrocopies	retro_sara_28, retro_sara_510,
Tupaia belangeri	ENSTBEG00000008608	1 retrocopy	retro_tbel_2485,