RetrogeneDB ID: retro_fcat_1817

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:45673510..45674055(+)
• Located in intron of: ENSFCAG00000001870

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL39
• Ensembl ID: ENSFCAG00000022879
• Aliases: None
• Description: mitochondrial ribosomal protein L39 [Source:HGNC Symbol;Acc:14027]

Sequence

>retro_fcat_1817
GCATTCAAAGATGAATGTGTGGTCAGTTTGGTCAGAGCTCCAGAGGTTTCTGTAATCTCTGGAGCCTTCTGCTATGATGC
AGTTCTGGATAAGAGACGTGATAAGTGGATGCCAACAAAAGAGAACCTGTGTTCCTTCACAGAAGATGCTCGTGTTTTAA
TTTATAAACATCTTCCATTTGAAACTCTGGAAGTGGAAACAAAAATGACATTAGAGATATTTCAACACAGCAAGTATAAA
ATGGATTTCATAGAAGAGCAGTCATTTCAGAACCCTGAGAGAATAGTCAAGCTACACAGATTGGTCACTTCATTGATGTG
AGTGAGGATCCTTTTAGTCCAAGAACAAGTATTTGTTTCCATTAGGAAGTGTCAGCAGTTCACAATCTTCAAACCACCCA
GTTGAGTCTTGTATGAAGAATCCAGGGTCTGTCTTTACCTATACACTTAAGAGCACATGTTACAATATGGGATAAGTCAT
TGGAAAGATCTTGGAAAATGCTAACTGAAGCTCAAACTAAACCTACAGAGGAAAATGTACCGACC

Alignment

ORF - retro_fcat_1817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.69 %
• Parental protein coverage: 54.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFKDEYVVSLVRAPEVPVISGAFCYDVVLDKRLDEWMPTKENLRSFTKDARALIYKDLPFETLEVEAKVA
          AFKDE.VVSLVRAPEV.VISGAFCYD.VLDKR.D.WMPTKENL.SFT.DAR.LIYK.LPFETLEVE.K..
Retrocopy AFKDECVVSLVRAPEVSVISGAFCYDAVLDKRRDKWMPTKENLCSFTEDARVLIYKHLPFETLEVETKMT

Parental  LEIFQHNKYKTDFIEEKASQNPERIVKLHR-FGDFIDVSEGPLIPRTSICFQYEVSAVHNLQATQLSLVR
          LEIFQH.KYK.DFIEE...QNPERIVKLHR..G.FIDVSE.P..PRTSICF..EVSAVHNLQ.TQLSLV.
Retrocopy LEIFQHSKYKMDFIEEQSFQNPERIVKLHR<IGHFIDVSEDPFSPRTSICFH*EVSAVHNLQTTQLSLV*

Parental  RFQGLSLPVHLRAHFTLWNKLLERSRKMVTEDQTKPTEESAST
          R.QGLSLP.HLRAH.T.W.K.LERS.KM.TE.QTKPTEE...T
Retrocopy RIQGLSLPIHLRAHVTIWDKSLERSWKMLTEAQTKPTEENVPT

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	16.99 RPM
SRP017611_kidney	0.10 RPM	26.49 RPM
SRP017611_liver	0.00 RPM	20.02 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1817 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1817 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
Felis catus	ENSFCAG00000022879	2 retrocopies	retro_fcat_1817 , retro_fcat_300,
Macropus eugenii	ENSMEUG00000002198	1 retrocopy	retro_meug_682,
Myotis lucifugus	ENSMLUG00000015959	1 retrocopy	retro_mluc_2403,
Tupaia belangeri	ENSTBEG00000006067	2 retrocopies	retro_tbel_2146, retro_tbel_4725,