RetrogeneDB ID: retro_fcat_1357

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:93762059..93762464(-)
• Located in intron of: ENSFCAG00000007116

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASF1A
• Ensembl ID: ENSFCAG00000023561
• Aliases: None
• Description: anti-silencing function 1A histone chaperone [Source:HGNC Symbol;Acc:20995]

Sequence

>retro_fcat_1357
CTCTTAGTGGGCCCTGTTTCTGCAGGACGGCATGTTTTATTTCCAGCTGAGGCACCTAATCCAAGACTCATTCCAGATGT
AGATGCAGTAGGTATAACAGTTGTGCTAATTACATGCACCTATTGAGGGCAAGAATTTATTAGAGTTGGCTGCCATGTAA
ATAATGAATATGTTGAGACAGAAGTATGGGAAAATTTGCCAGGAAAACCAGACTTTTCTAAGCTTCAAAGGAACATTTTG
GCACCTAATCCTAGAGTCACGAGAGTTCACATTATATGGGAAGACAATATAGAAAAACTGGAAGAGGCAGAGATCAGTAA
TCCAAATCTATAATTACCTCTTTCAACAGATGCATTACCTTCAGCATCAAAGGGATGGATGGCCTATGTCAAAAAACTGA
CTATT

Alignment

ORF - retro_fcat_1357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 66.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLVGPVPAGRHMFVFQADAPNPGLIPDADAVGVTVVLITCTYRGQEFIRVGYYVNNEYTETELRENPPVK
          .LVGPV.AGRH...F.A.APNP.LIPD.DAVG.TVVLITCTY.GQEFIRVG..VNNEY.ETE..EN.P.K
Retrocopy LLVGPVSAGRHV-LFPAEAPNPRLIPDVDAVGITVVLITCTY*GQEFIRVGCHVNNEYVETEVWENLPGK

Parental  PDFSKLQRNILASNPRVTRFHINWEDNTEKLEDAESSNPNLQSLLSTDALPSASKGWSTSENSLNV
          PDFSKLQRNILA.NPRVTR.HI.WEDN.EKLE.AE.SNPNL...LSTDALPSASKGW......L..
Retrocopy PDFSKLQRNILAPNPRVTRVHIIWEDNIEKLEEAEISNPNL*LPLSTDALPSASKGWMAYVKKLTI

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	14.94 RPM
SRP017611_liver	0.00 RPM	6.47 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1357 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1357 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013007	1 retrocopy	retro_chof_496,
Felis catus	ENSFCAG00000023561	1 retrocopy	retro_fcat_1357 ,
Myotis lucifugus	ENSMLUG00000013053	1 retrocopy	retro_mluc_1410,
Otolemur garnettii	ENSOGAG00000034346	1 retrocopy	retro_ogar_2054,
Ochotona princeps	ENSOPRG00000004979	1 retrocopy	retro_opri_416,
Tupaia belangeri	ENSTBEG00000000592	2 retrocopies	retro_tbel_2900, retro_tbel_4175,