RetrogeneDB ID: retro_fcat_1478

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D2:37171093..37171402(+)
• Located in intron of: ENSFCAG00000015570

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD1
• Ensembl ID: ENSFCAG00000001235
• Aliases: None
• Description: pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha [Source:HGNC Symbol;Acc:8646]

Sequence

>retro_fcat_1478
GCTGGCAAAACACAGAGGCTAAGTGATGAGGAGAGGAACCAGCTGTTGGCAAACCTGAGAGCTCTAGGGTGGAAGGAGCT
GGAAGGCAGAGATGCTATCTTCAAGCAGTTCCATTTCAAAGACTTCATTTGGGCCTTTGGCTTCATGATGAGGGTGGCCC
TGCAGGCTCAGAAACCAGACCACCATCCCGAATGGTTTAACATGTACAGTAAGGCCCACATCACCCTGAGCACCCGTGAA
TGTGCAGGCCTTTTAGAACAGGACATAAACCTGGCCAGCTTCATCGAACAAGTAGCAGTGTCCATGACA

Alignment

ORF - retro_fcat_1478 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGKAHRLSAEERDQLLPNLRAVGWNELEGRDAIFKQFHFKDFNRAFGFMTRVALQAEKLDHHPEWFNVYN
          AGK..RLS.EER.QLL.NLRA.GW.ELEGRDAIFKQFHFKDF..AFGFM.RVALQA.K.DHHPEWFN.Y.
Retrocopy AGKTQRLSDEERNQLLANLRALGWKELEGRDAIFKQFHFKDFIWAFGFMMRVALQAQKPDHHPEWFNMYS

Parental  KVHITLSTHECAGLSERDINLASFIEQVAVSMT
          K.HITLST.ECAGL.E.DINLASFIEQVAVSMT
Retrocopy KAHITLSTRECAGLLEQDINLASFIEQVAVSMT

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	0.57 RPM	1.61 RPM
SRP017611_kidney	3.30 RPM	54.83 RPM
SRP017611_liver	10.61 RPM	67.53 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1478 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1478 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011866	1 retrocopy	retro_btau_1478,
Cavia porcellus	ENSCPOG00000012703	1 retrocopy	retro_cpor_61,
Felis catus	ENSFCAG00000001235	1 retrocopy	retro_fcat_1478 ,
Loxodonta africana	ENSLAFG00000001397	1 retrocopy	retro_lafr_1028,
Myotis lucifugus	ENSMLUG00000016074	3 retrocopies	retro_mluc_1534, retro_mluc_2459, retro_mluc_462,
Procavia capensis	ENSPCAG00000007201	1 retrocopy	retro_pcap_46,
Sus scrofa	ENSSSCG00000010275	1 retrocopy	retro_sscr_744,
Takifugu rubripes	ENSTRUG00000017869	1 retrocopy	retro_trub_26,
Tursiops truncatus	ENSTTRG00000005775	1 retrocopy	retro_ttru_1541,
Vicugna pacos	ENSVPAG00000004496	1 retrocopy	retro_vpac_69,