RetrogeneDB ID: retro_fcat_1218

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:142041030..142041400(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM168B
• Ensembl ID: ENSFCAG00000000303
• Aliases: None
• Description: family with sequence similarity 168, member B [Source:HGNC Symbol;Acc:27016]

Sequence

>retro_fcat_1218
GTCACACCTTACACAGTATTCTGTCCCCCCACCAATGGGGCAGTGCCACCATACTCCTCTTCCCCTACCAAAATGCCTAC
CCCCCAAGAGAGCCCCTATGCACACACAGCCCCAGTAGGCAGTGCCCCCTCACATCATCCACCACACCACAGTTGTGCAG
CCCAACTGCATGCTGGTGGTGATTTACCCCGATCCCATCCCTCTACTTAGAGGCAATGGTGTCACCATGGGTATGGTGGC
TGGGACCACTGTGGCCATGTCAGCAGGTACCCTCCTGACCTTCCATACCTCAACTCCTGTTGCCCCCATGCACTGTGCCC
ACGTATCTGGCCCCAGGGGCCCCACTTATAGCTAGGTTCCCCCTCAGTGG

Alignment

ORF - retro_fcat_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.38 %
• Parental protein coverage: 64.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPPYSSSPNPYQTAVYPVRSAYPQQSPYAQQGTY-YTQPLYAAPPHVIHHTTVVQPNGMPATVYPAPIPP
          V.PY.....P...AV.P..S..P...P..Q...Y..TQP..A.PPH.IHHTTVVQPN.M....YP.PIP.
Retrocopy VTPYTVFCPPTNGAVPPYSSS-PTKMPTPQESPY>HTQPQ*AVPPHIIHHTTVVQPNCMLVVIYPDPIPL

Parental  PRGNGVTMGMVAGTTMAMSAGTLLTAHSPTPVAP-HPVTVPTYRAPGTPTYSYVPPQW
          .RGNGVTMGMVAGTT.AMSAGTLLT.H..TPVAP.H...V...R.P...TYS.VPPQW
Retrocopy LRGNGVTMGMVAGTTVAMSAGTLLTFHTSTPVAPMHCAHVSGPRGP---TYS*VPPQW

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	19.05 RPM
SRP017611_kidney	0.00 RPM	4.23 RPM
SRP017611_liver	0.00 RPM	2.73 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1218 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1218 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004222	2 retrocopies	retro_cfam_1748, retro_cfam_344,
Choloepus hoffmanni	ENSCHOG00000009590	1 retrocopy	retro_chof_551,
Equus caballus	ENSECAG00000017018	1 retrocopy	retro_ecab_27,
Felis catus	ENSFCAG00000000303	1 retrocopy	retro_fcat_1218 ,
Monodelphis domestica	ENSMODG00000018633	1 retrocopy	retro_mdom_1625,
Mustela putorius furo	ENSMPUG00000011824	1 retrocopy	retro_mputfur_454,
Ictidomys tridecemlineatus	ENSSTOG00000000206	2 retrocopies	retro_itri_191, retro_itri_262,
Tupaia belangeri	ENSTBEG00000017162	1 retrocopy	retro_tbel_83,