RetrogeneDB ID: retro_fcat_1224

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:158483712..158483998(-)
• Located in intron of: ENSFCAG00000030802

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL52
• Ensembl ID: ENSFCAG00000006625
• Aliases: None
• Description: mitochondrial ribosomal protein L52 [Source:HGNC Symbol;Acc:16655]

Sequence

>retro_fcat_1224
AGGCAGAGCCTGGCTACCAACCCCTCTGGCTACAGACCCTTTACAGAGTTCCCAGACTGATCTTACACAGATGGCCGCCC
TGTACCTCCAATGAAAGGCCAGCTTTGAAGAAAAGCCCAAAGGGAGATGTTTGCAAGATGAGTTGCACTGCTATCACAGA
AAATGGATGCTGGATTACAGTCATGGCAACTTAGACAGCAGGAGAAGTTGCAGGAAGAAGAAAGGAGGCAGAAAAAGGCT
CTTAAAACCCAAAGACGCTCTACTGCAGAACCCACAACTAAGTCAA

Alignment

ORF - retro_fcat_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 76.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QQGLAANPSGYGPLTELPDWSYADGRPAPPMKGQLRRTAQREKFARRVVLLSQEMDAGLQAWQLRQQ-KL
          .Q.LA.NPSGY.P.TE.PD.SY.DGRP.PPMKGQL.R.AQRE.FAR.V.LLSQ.MDAGLQ.WQLRQQ.KL
Retrocopy RQSLATNPSGYRPFTEFPD*SYTDGRPVPPMKGQL*RKAQREMFAR*VALLSQKMDAGLQSWQLRQQEKL

Parental  QEEEGKQKNA-LKPKGALLQNPLPSQ
          QEEE..QK.A.LKPK.ALLQNP..SQ
Retrocopy QEEERRQKKA>LKPKDALLQNPQLSQ

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	3.79 RPM
SRP017611_kidney	0.00 RPM	15.15 RPM
SRP017611_liver	0.00 RPM	10.01 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1224 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1224 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007264	1 retrocopy	retro_amel_523,
Bos taurus	ENSBTAG00000014822	1 retrocopy	retro_btau_1839,
Felis catus	ENSFCAG00000006625	1 retrocopy	retro_fcat_1224 ,
Tupaia belangeri	ENSTBEG00000000986	1 retrocopy	retro_tbel_1871,