RetrogeneDB ID: retro_fcat_2002

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:82673020..82673463(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC3
• Ensembl ID: ENSFCAG00000024898
• Aliases: None
• Description: ER membrane protein complex subunit 3 [Source:HGNC Symbol;Acc:23999]

Sequence

>retro_fcat_2002
AATGAACCAAATGCCCTCCCTATGATTCTTATTGGTTAATGGATCAGCATTATATTTTCAGGCTCTATCACAAGGCAAGA
TCTCTTTTTCACTGACCCATCATTTTAAATCTAGACTACAGCAATGAATCAAGCTATTTTCATTAGATGCATTCTGGATT
AGTTCTGCATCCTGGTATTTCACCAATGTATTTGGGCTTCAGAGCATTTACTCTGATTTTGGGCCAAGATGCTGCTGCTG
GCCAATCACATATGACTCAGCAGCAGAAAACTAGAGCCACCAAGAACATGCCCACAGACAATAACAAAGCTTTCAAGACA
GAGTAGGAACCTATAGAACTGGCACATCACCAGCAGGCACTAGATAATGTTGAAGAGGAGCTCATGACCAAAGACCTCCA
CTTTGAAAGCATGTTCAAAAAGGAATCATAGACCTCTATTTTT

Alignment

ORF - retro_fcat_2002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64. %
• Parental protein coverage: 56.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NVTNVLPMILIGGWINMTFSGFVTT-KVPFPLTLRFKPMLQQGIELLTLDASWVSSASWYFLNVF-GLRS
          N..N.LPMILIG.WI...FSG..T..K..F.LT..FK..LQQ.I.L..LDA.W.SSASWYF.NVF.G.R.
Retrocopy NEPNALPMILIG*WISIIFSGSITR>KISFSLTHHFKSRLQQ*IKLFSLDAFWISSASWYFTNVF>GFRA

Parental  IYSLILGQDNAADQSRMMQEQMTGAAMAMPADTNKAFKTEWEALELTDHQWALDDVEEELMAKDLHFEGM
          ...LILGQD.AA.QS.M.Q.Q.T.A...MP.D.NKAFKTE.E..EL..HQ.ALD.VEEELM.KDLHFE.M
Retrocopy -FTLILGQDAAAGQSHMTQQQKTRATKNMPTDNNKAFKTE*EPIELAHHQQALDNVEEELMTKDLHFESM

Parental  FKKELQTSIF
          FKKE..TSIF
Retrocopy FKKES*TSIF

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	80.46 RPM
SRP017611_kidney	0.00 RPM	86.77 RPM
SRP017611_liver	0.00 RPM	60.35 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_2002 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_2002 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005202	1 retrocopy	retro_cfam_730,
Callithrix jacchus	ENSCJAG00000037305	1 retrocopy	retro_cjac_3209,
Equus caballus	ENSECAG00000024410	1 retrocopy	retro_ecab_737,
Felis catus	ENSFCAG00000024898	2 retrocopies	retro_fcat_1932, retro_fcat_2002 ,
Microcebus murinus	ENSMICG00000002333	2 retrocopies	retro_mmur_439, retro_mmur_707,
Mustela putorius furo	ENSMPUG00000017149	1 retrocopy	retro_mputfur_456,
Pteropus vampyrus	ENSPVAG00000012615	3 retrocopies	retro_pvam_1260, retro_pvam_1278, retro_pvam_1439,
Tursiops truncatus	ENSTTRG00000007554	2 retrocopies	retro_ttru_1311, retro_ttru_285,
Vicugna pacos	ENSVPAG00000003247	2 retrocopies	retro_vpac_308, retro_vpac_461,