RetrogeneDB ID: retro_fcat_1393

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:42133004..42133540(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLS1
• Ensembl ID: ENSFCAG00000023647
• Aliases: None
• Description: cardiolipin synthase 1 [Source:HGNC Symbol;Acc:16148]

Sequence

>retro_fcat_1393
AACCCACGGACAATTCCATGTATGTTGTCAATGACGAGAATCAACTTGGCCCCAGTTTGGGGCTCTTGGATTACTGGAGA
AGATTTTGGTGTTGCCCAAGGAGTTTTTGCGTTTGTTGGGTTCACTGATCTGTTGGGTGGATTTATTGCTTGAAATTGAG
ACAACTGTGAGTCAATTTGGGAAACGTTCTTGGTCCACTTGCTGGTAAAATGCCAATGGCACCCTATATATTAGCTTGAT
CTATGCAAGTCTTACTCCAGTTTCACTTGCTTGCATGATAACGTCACAGATGTAATATTGGTGGCTACCAATATTTTTAT
GTCCGTTATTGAATTCTTCCAGTGCTGAGAACAGTTGCTAAGTTTTTCAATCCTTGCTGTGTCACTGCTAAATTAAAGCC
AACGTTCGTCAGCAAAGTAAACATCGCAGCCCGGTTGATTTGGGCAGTTTCTTTGGCTCCGCTGCTGTTCAGTTATGCTG
ACAGGATTCATCTTCAGACGTGGTGTTTGATATTTTGCAGCACAGCTGCCTCAGCT

Alignment

ORF - retro_fcat_1393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.06 %
• Parental protein coverage: 89.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NPWTIPNMLSMTRIGLAPVLGYLIIEEDFNIALGVFALAGLTDLLDGFIARNWANQKSA-LGSALDPLAD
          NP.TIP.MLSMTRI.LAPV.G..I..EDF..A.GVFA..G.TDLL.GFIA.N..N..S..LG..L.PLA.
Retrocopy NPRTIPCMLSMTRINLAPVWGSWITGEDFGVAQGVFAFVGFTDLLGGFIA*N*DNCESI<LGNVLGPLAG

Parental  KILIS-ILYVSLTYADLIPVPLTYMIISR-DVMLIAA-VF-YVRYRTLPTPRTLSKYFNPCYATARLKPT
          K......LY.SL.YA.L.PV.L..MI.S..DV.L.A...F.YVRY..LP..RT..K.FNPC..TA.LKPT
Retrocopy KMPMA<TLYISLIYASLTPVSLACMITSQ<DVILVATNIF<YVRY*ILPVLRTVAKFFNPCCVTAKLKPT

Parental  FISKVNTAVQLILVAASLAAPVFNYADSIYLQILWCFTAFTTAASA
          F.SKVN.A..LI..A.SLA...F.YAD.I.LQ..WC.....TAASA
Retrocopy FVSKVNIAARLIW-AVSLAPLLFSYADRIHLQ-TWCLIFCSTAASA

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	14.00 RPM
SRP017611_kidney	0.00 RPM	48.23 RPM
SRP017611_liver	0.00 RPM	48.93 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1393 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1393 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010596	1 retrocopy	retro_amel_1758,
Bos taurus	ENSBTAG00000000065	1 retrocopy	retro_btau_1167,
Canis familiaris	ENSCAFG00000005934	1 retrocopy	retro_cfam_1002,
Equus caballus	ENSECAG00000023869	2 retrocopies	retro_ecab_247, retro_ecab_930,
Felis catus	ENSFCAG00000023647	1 retrocopy	retro_fcat_1393 ,
Microcebus murinus	ENSMICG00000011666	1 retrocopy	retro_mmur_751,
Mustela putorius furo	ENSMPUG00000006349	1 retrocopy	retro_mputfur_1021,
Rattus norvegicus	ENSRNOG00000021273	3 retrocopies	retro_rnor_2865, retro_rnor_2866, retro_rnor_2977,