RetrogeneDB ID: retro_fcat_570

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:136345929..136346698(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSFCAG00000026288
• Aliases: None
• Description: ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]

Sequence

>retro_fcat_570
ATGGGCCACATAATTCTGGGGTAGAGGAAGGATGCTGGCTCAGTGTTCCATGCCCACATGAAGCATGGCAAGGGTGCTGC
ATGTCTGCTTGCCATGGACTTTGCAGAGAAGTTGGGCTACATCAGGGGCATCATGAAGGACATTATTCATGACCAGGGTG
GAGGTGAACCCCTCACTGAGGTAGTCTTCTGAGATCTGTACTGGTTTAAGAAGTGGCAGGAGCTGTTCATCACCCCCAAT
GGCATCTACACTGGCTATTTTGTGTACTGTGGCAAGAAGGCCCAGCTCAACATAGGCAATGTGCTCCTAGTGGGCACTAT
GCCCAAGGTCACCATTGTGTATTGTTTGGAGGAGAAGCTTGGTGACTTGGCAAGTTGGCCCAAGCCTCTGGGAATGATGC
TACTTCATCTCCCACAACCCTGAGACCAAAGAAGACCCAAGTGAAGCTGTCCTCAGCCACCTGAGAAATCAAGGTCATTT
CTTCAGCCAATAGAACTATGTTGATGTGGTGGCTGGAGGTGGCCACGTTGACAAGACCATTCTGAAGGCTGGCTGTGCCT
ACCACAAGTATAAGGCAAAGAGGAGTTGCTGACCACACATACTGGGTGTGGCTATGAATCCTGTGGGAACATCCTTTTGG
AGGTGGCAAGCACCAGCACATCACAAACCCTGTACTATCTGTAGAGATACCCCTGCTGGCTGCATAGTGGGTCTTATTGC
TGCCTACCAGACCTCTGGGAGAACCTAGACTGTGTAGGAGAAAGAGAAC

Alignment

ORF - retro_fcat_570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFK
          MG..I.G.RK.AGSVF.AH.KH.KGAA.L.A.DFAE..GYI.GI.KDIIHD.G.G.PL..VVF.D.Y.FK
Retrocopy MGHIILG*RKDAGSVFHAHMKHGKGAACLLAMDFAEKLGYIRGIMKDIIHDQGGGEPLTEVVF*DLYWFK

Parental  KRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGD-RGKLARASGNYAT-VIS
          K..ELFI...GI.TG.FVYCGKKAQLNIGNVL.VGTMP..TIV.CLEEK.GD..GKLA.ASGN.AT..IS
Retrocopy KWQELFITPNGIYTGYFVYCGKKAQLNIGNVLLVGTMPKVTIVYCLEEKLGD<LGKLAQASGNDAT<FIS

Parental  HNPET-KKTRVKLPSGS--KKVISSANRAV-VGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAM
          HNPET.KKT.VKL.S.....KVISSANR...V.VVAGGG..DK.ILKAG.AYHKYKAKR.C.P...GVAM
Retrocopy HNPET>KKTQVKLSSAT*EIKVISSANRTM<VDVVAGGGHVDKTILKAGCAYHKYKAKRSC*PHILGVAM

Parental  NPV-EHPFGGGNHQHI-GKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN
          NPV.EHPFGGG.HQHI..KP.TI.RD.PAG..VGLIAA..T.....T.TV.EKEN
Retrocopy NPV>EHPFGGGKHQHI<HKPCTICRDTPAGCIVGLIAAYQTS--GRT*TV*EKEN

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	86.88 RPM
SRP017611_kidney	0.00 RPM	295.88 RPM
SRP017611_liver	0.00 RPM	155.48 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_570 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_570 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Echinops telfairi	ENSETEG00000007104	4 retrocopies	retro_etel_1100, retro_etel_264, retro_etel_296, retro_etel_916,
Felis catus	ENSFCAG00000026288	1 retrocopy	retro_fcat_570 ,
Homo sapiens	ENSG00000161016	1 retrocopy	retro_hsap_2851,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,