RetrogeneDB ID: retro_fcat_300

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:216514962..216515634(-)
• Located in intron of: None

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_300
CCACGAACTGAGAAGAGTGAAGCTAAACACGTTGAGAAAAATGATGCTGACCCTATTTTGTGATGAACAAAACCATTTCA
ACTCTTTACAATTTGCCAGGCATCTGAGTGGGTGGTAATCCTGGAAGTCCCTTCCAGCTCTTGTGGACAAACAGCCTTGG
GACATGTACACCCCGGTGACCAAGTCCCGAGGAATTTAGTTTCTTACTTTCAAAGGTCATGAGCAAGGAGAAGTGAATAC
GTCTTATGGGCATTCTTGTGCCATGATGATGGACTGTATGACAGAGAGGGCATTGGAAAGTGAACATGTGGTCAGTTTGT
TCAGAGCTCCAGAGGTTCCTGCAATCTTTGGAGCCTTCTGTTATGATACAGTTTTAGAGAAGGGACTTGATGAGTGGATG
CCAACAAAAGAGAATCTACATTCCTTCACCAAAGAGGCTTGCCCTTTGACTTATAAAGATCTTCCATTCGAAACGCTGGA
AGTTGAAGTAAATTGGCATTGGAAAGACTTTAACACAACAAGCACAAAATAGATCTCGTAGAAGAGAAGGCATCTGGGAA
TCCTGAGAACATCATCCAGCTACACAGATTTGATGACTTAATTGTTGTGAGGAAGGGTCCTCTTAGTCCAAGAACAAATA
TGTGTTCCTGTTATGTAGCATCAGCAGACCAC

Alignment

ORF - retro_fcat_300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.35 %
• Parental protein coverage: 66.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PRTEKIEVKHVGKTDPGTI-FVMNKNISTPYSC-AMHLSEWYCGKSILALVDGQPWDMYKPLTKSCEIEF
          PRTEK.E.KHV.K.D...I.FVMNK.IST.Y...A.HLS.W...KS..ALVD.QPWDMY.P.TKS..I.F
Retrocopy PRTEKSEAKHVEKNDADPI<FVMNKTISTLYNL<ARHLSGW*SWKSLPALVDKQPWDMYTPVTKSRGI*F

Parental  LTFKDRDPGEVNKAYWRSCAMMMGCVIERAFKDEYVVSLVRAPEVPVISGAFCYDVVLDKRLDEWMPTKE
          LTFK....GEVN..Y..SCAMMM.C..ERA...E.VVSL.RAPEVP.I.GAFCYD.VL.K.LDEWMPTKE
Retrocopy LTFKGHEQGEVNTSYGHSCAMMMDCMTERALESEHVVSLFRAPEVPAIFGAFCYDTVLEKGLDEWMPTKE

Parental  NLRSFTKDARALIYKDLPFETLEVE-AKVALEIFQHNKYKTDFIEEKASQNPERIVKLHRFGDFIDVSEG
          NL.SFTK.A..L.YKDLPFETLEVE..K.ALE...HNK.K.D..EEKAS.NPE.I..LHRF.D.I.V..G
Retrocopy NLHSFTKEACPLTYKDLPFETLEVE<SKLALERL*HNKHKIDLVEEKASGNPENIIQLHRFDDLIVVRKG

Parental  PLIPRTSICFQYEVSAVH
          PL.PRT..C..Y..SA.H
Retrocopy PLSPRTNMCSCYVASADH

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	0.00 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_300 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_300 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,