RetrogeneDB ID: retro_fcat_639

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:102058459..102058853(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL16
• Ensembl ID: ENSFCAG00000007540
• Aliases: None
• Description: mitochondrial ribosomal protein L16 [Source:HGNC Symbol;Acc:14476]

Sequence

>retro_fcat_639
GATTCTTGGGCAGCCCCACCTGCCAGTGCTGGACTATGGATGCTGCTCCTGGTGCCAACTCTTGAGGATGTTTCCATTCT
TGAAAAGCCCAAGTTTAAATTTGTTGAAAGGGCAACATCTGTGTGTGCCAAAAGTGAGAGGAGAACTTAAAAGCGACATA
TGAGGACCTTCTACTGAAGCTACTGAGTTCACAGAAGGCAGTTGTGCGATCTTGGCACTGGGTGGTGGTCACCTCCATTG
GAGCCATTTTGAAATGATGCACCTGACAAAGTACTGCTCTGTGGACCCTAAGAACATATTTGCCTTATGAAGAGTACTAG
CCCCTTTTCAGCCCATCACCTGCAAGGGTATGACACACATGGGAGCCAAAGGTGCCATTGATCATTACATGACT

Alignment

ORF - retro_fcat_639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.65 %
• Parental protein coverage: 57.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSWVASPASAGLKTLLPVPAFEDVSIPEK-PKLRFVERVPL-VPKVRREPKNLSDIRGPSAEATEFTEGS
          DSW.A.PASAGL..LL.VP..EDVSI.EK.P.L.......L.VPKVR.E.K..SDI.GPS.EATEFTEGS
Retrocopy DSWAAPPASAGLWMLLLVPTLEDVSILEK>PSLNLLKGQHLCVPKVRGELK--SDI*GPSTEATEFTEGS

Parental  FAILALGGGYLHWGHFEMMRLTINRSLDPKNMFALWRVPAPFKPITRKGMGQRMGGGKGAIDHYVT
          .AILALGGG.LHW.HFEMM.LT...S.DPKN.FAL.RV.APF.PIT.KGM.....G.KGAIDHY.T
Retrocopy CAILALGGGHLHWSHFEMMHLTKYCSVDPKNIFAL*RVLAPFQPITCKGMTHM--GAKGAIDHYMT

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	20.43 RPM
SRP017611_kidney	0.00 RPM	49.67 RPM
SRP017611_liver	0.00 RPM	21.03 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_639 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_639 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014289	1 retrocopy	retro_amel_1231,
Canis familiaris	ENSCAFG00000031711	2 retrocopies	retro_cfam_393, retro_cfam_865,
Dipodomys ordii	ENSDORG00000015111	1 retrocopy	retro_dord_389,
Felis catus	ENSFCAG00000007540	2 retrocopies	retro_fcat_479, retro_fcat_639 ,