RetrogeneDB ID: retro_fcat_1558

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D3:65768642..65768860(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC167
• Ensembl ID: ENSFCAG00000006745
• Aliases: None
• Description: coiled-coil domain containing 167 [Source:HGNC Symbol;Acc:21239]

Sequence

>retro_fcat_1558
AATCTGGGCATTGCTCTAGAGATGGAGGAGATGGAGGAGAAGGTGTCACAGTGCAGTAGGCACCTGGAGGCTGTAAACTC
TAGGCTCTGAGGCAGAGATAAACCCAAATGGCCAAGAAGTCTCTAGAGAAGGAGAAAAACAGCCTGATGAACAAAGCCTC
CAACTATGAGAAGAAACTAAAGTTGCTTCAGCAGGAGAACTGGTAGAACATGTTGCTC

Alignment

ORF - retro_fcat_1558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.81 %
• Parental protein coverage: 81.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLGCLQQIDGLEEKLSQCRKDLEAVNSRLCGTEL-SPETRKSLEKEKNSLMNKASNYEKELKLLRQENRK
          NLG............SQC...LEAVNSRL.G.........KSLEKEKNSLMNKASNYEK.LKLL.QEN..
Retrocopy NLGIALXXXXXXXXVSQCSRHLEAVNSRL*GRDK<TQMAKKSLEKEKNSLMNKASNYEKKLKLLQQENW*

Parental  NMLL
          NMLL
Retrocopy NMLL

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	1.61 RPM
SRP017611_kidney	0.00 RPM	2.37 RPM
SRP017611_liver	0.00 RPM	5.46 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1558 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1558 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012069	2 retrocopies	retro_btau_30, retro_btau_517,
Canis familiaris	ENSCAFG00000030835	1 retrocopy	retro_cfam_1854,
Callithrix jacchus	ENSCJAG00000005622	2 retrocopies	retro_cjac_3293, retro_cjac_960,
Felis catus	ENSFCAG00000006745	1 retrocopy	retro_fcat_1558 ,
Mus musculus	ENSMUSG00000024018	1 retrocopy	retro_mmus_3487,
Otolemur garnettii	ENSOGAG00000000921	1 retrocopy	retro_ogar_880,
Pongo abelii	ENSPPYG00000016563	1 retrocopy	retro_pabe_2092,