RetrogeneDB ID: retro_fcat_1195

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:77242757..77243218(-)
• Located in intron of: ENSFCAG00000027703

Retrocopy information

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

Parental gene information

• Parental gene symbol: REEP4
• Ensembl ID: ENSFCAG00000009632
• Aliases: None
• Description: receptor accessory protein 4 [Source:HGNC Symbol;Acc:26176]

Sequence

>retro_fcat_1195
ACCTGCATCGTGCACGCCAAGGAATGCAGCTATGAGATGATGCTCAGCTTTGGGAAACGGGGGTCTCAACATTGCTGCTT
CGACTGCTGTACAGCCTACCACCAAGAGTCAGGGTGCACTGGCTGGAAGGCTGCGGAGCTTCTCCATACAGGACCTGCAC
TCCATCCCTGATGCCCCTGCCCCCTGCCTACCAGCATCCCCTCTACATGGAGGACCAGGTACCTCACCTCAGGCCGCCCA
TCAGTTATAGAGCAGGGGGCCTGCAGGACAGCGACACTGAGGATGAGTGTTGGTCAGGTACAGAGGCAGTCTCTCAGCCA
CCTGCCTGACCCCGAGAGAAGCCTCTGAGCTGCAGCCAGAACCTGCGTGTGGTTAAGAGGAAGCCACCCATGTGGGAGGG
CACTTCACACTCACTGAGGATTCAGAAAAGGAAAAAGACCATTTCCTCAGACATGAACAGC

Alignment

ORF - retro_fcat_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 59.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TCIVQAKERSYETMLSFGKRG-LNIAASAAVQAATKSQGALAGRLRSFSMQDLRSIPDAPAP-AYQDPLY
          TCIV.AKE.SYE.MLSFGKRG.LNIAAS.AVQ..TKSQGALAGRLRSFS.QDL.SIPDAPAP.AYQ.PLY
Retrocopy TCIVHAKECSYEMMLSFGKRG>LNIAASTAVQPTTKSQGALAGRLRSFSIQDLHSIPDAPAP>AYQHPLY

Parental  LEDQVPRRRPPIGYRAGGLQDSDTEDECWSDTEAVSQPPARPREKPLSRSQSLRVVKRKPPMREGTSRSL
          .EDQVP..RPPI.YRAGGLQDSDTEDECWS.TEAVSQPPA.PREKPLS.SQ.LRVVKRKPPM.EGTS.SL
Retrocopy MEDQVPHLRPPISYRAGGLQDSDTEDECWSGTEAVSQPPA*PREKPLSCSQNLRVVKRKPPMWEGTSHSL

Parental  KVRTRKKTISSDMNS
          ....RKKTISSDMNS
Retrocopy RIQKRKKTISSDMNS

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	1.26 RPM
SRP017611_kidney	0.21 RPM	2.99 RPM
SRP017611_liver	0.30 RPM	7.99 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1195 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1195 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020323	1 retrocopy	retro_cjac_744,
Felis catus	ENSFCAG00000009632	1 retrocopy	retro_fcat_1195 ,