RetrogeneDB ID: retro_fcat_1418

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:87731213..87731719(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000027672
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CIDEB
• Ensembl ID: ENSFCAG00000026821
• Aliases: None
• Description: cell death-inducing DFFA-like effector b [Source:HGNC Symbol;Acc:1977]

Sequence

>retro_fcat_1418
ATCAAAGGTGCCAGCTGCCAAGAACTGCTAGACAAGGTGATGGAGACCCTACAGCTGACAGGAATGCTAACACAGGTGCT
AGAGGAGGATGGGACCTCCATGGAGAGCAAGGACTTCTTCCAGCTGCTGGAAGAAGACACAGGCCTGATGGTGCTGGAGT
TTGGGGAAAGCTGGACCCCAGCAGAAATGGGTACTGTCATATGGGCTGGGCCAGAAGAACCCCAAGCACAGAAAGGACAT
CACCCTCATCACTTTCCGTGTATACAAGCAAAACCCTTGGGACTTCTTTGGCAGCCTGACATCAAAGCCACATTCTACAG
GCTCTACTCCACAAGCTGACTCTAAAGGACTTGGCCCAAAGAAAGTACTCAGGGAGCTCCTTCAGTTGGACCTCCACGTT
GTCACAAGGCCTGGGCCACATGTTGCTGGGAATTTCCTCCATCATTCACCATTCAGTAGAGGAGGCTAAGCAGTGGCAGC
AGCAGCAACACGGTGGCCTCCATCCC

Alignment

ORF - retro_fcat_1418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.32 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTAATRQELLDKALEALLLSGMLTLVLEEDGTAVESEDFFQLLEDDTCLMVLEYGQSWTP-SRSG-VLSY
          ...A..QELLDK..E.L.L.GMLT.VLEEDGT..ES.DFFQLLE.DT.LMVLE.G.SWTP.SR.G.VLSY
Retrocopy IKGASCQELLDKVMETLQLTGMLTQVLEEDGTSMESKDFFQLLEEDTGLMVLEFGESWTP<SRNG<VLSY

Parental  GLGREKPKHSKDIARITFDVYKQNPRDLFGSLNIKATFYGLYSMSCDFQGLGPKKVLRELLR-WTSALLQ
          GLG...PKH.KDI..ITF.VYKQNP.D.FGSL..K....G......D..GLGPKKVLRELL..WTS.L.Q
Retrocopy GLGQKNPKHRKDITLITFRVYKQNPWDFFGSLTSKPHSTGS-TPQADSKGLGPKKVLRELLQ>WTSTLSQ

Parental  GLGHMLLGISSSLRHLIEGAEQWHWQRQGRLHP
          GLGHMLLGISS...H..E.A.QW..Q..G.LHP
Retrocopy GLGHMLLGISSIIHHSVEEAKQWQQQQHGGLHP

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	0.11 RPM
SRP017611_kidney	0.00 RPM	20.51 RPM
SRP017611_liver	0.00 RPM	147.89 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1418 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1418 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016089	1 retrocopy	retro_amel_633,
Canis familiaris	ENSCAFG00000012240	1 retrocopy	retro_cfam_85,
Equus caballus	ENSECAG00000010495	1 retrocopy	retro_ecab_943,
Felis catus	ENSFCAG00000026821	1 retrocopy	retro_fcat_1418 ,
Pteropus vampyrus	ENSPVAG00000007036	1 retrocopy	retro_pvam_523,