RetrogeneDB ID: retro_fcat_42

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:86347649..86348087(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000023855
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000009220
• Aliases: None
• Description: None

Sequence

>retro_fcat_42
ATGAGATCTCTGTGGCTGCTCAGAACCCCCTTCATATGTGGCCTGCTCTGGGCTTTTTGTGCTCTGGGTACCAGGGCTGA
GGAGCCAGGGGCAAACTTTTCCCATCCCAACAGCATGGGCCTGGATAAGAACACAGTGCATGACCAAGAGCATATCATGG
AGTATCTAGAAGGTTTCATCAACAAACCGGAGGTAGAGATGTTCCCACAGGCACTGCACCTCCATTATTTCAAACTGCAT
GATTATGACAGCAATAATTTGCTTGACAGCCTAGAACTTTCCACAGTCATTGCTGGCATCCATAAGAAGGAAAAGGAACA
GGCACCACCAATGAGTGAAGCTGAACTGATTAACTTAATAGATGGTGTTTTGAGTGAGAATGACAAGAACAATAATGAAT
GTATTGACTGTGCTGAATTTGCCAAATCACTGAAATAG

Alignment

ORF - retro_fcat_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRSLRLLRTPFLCGLLWAFCAPGAGAEEPGASFSHPGSVGLDKNTVHDQEHIMEHLEGVINKPEAEMSPQ
          MRSL.LLRTPF.CGLLWAFCA.G..AEEPGA.FSHP.S.GLDKNTVHDQEHIME.LEG.INKPE.EM.PQ
Retrocopy MRSLWLLRTPFICGLLWAFCALGTRAEEPGANFSHPNSMGLDKNTVHDQEHIMEYLEGFINKPEVEMFPQ

Parental  ELQLHYFKMHDYDGNNLLDGLELSTAITHVHKEEANEQAPPMSEAELINLIDGVLRDDDKNNDGYIDYAE
          .L.LHYFK.HDYD.NNLLD.LELST.I...HK.E..EQAPPMSEAELINLIDGVL...DKNN...ID.AE
Retrocopy ALHLHYFKLHDYDSNNLLDSLELSTVIAGIHKKE-KEQAPPMSEAELINLIDGVLSENDKNNNECIDCAE

Parental  FAKSLQ
          FAKSL.
Retrocopy FAKSLK

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	10.56 RPM
SRP017611_kidney	0.00 RPM	20.71 RPM
SRP017611_liver	0.00 RPM	37.20 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_42 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_42 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006097	2 retrocopies	retro_amel_720, retro_amel_906,
Bos taurus	ENSBTAG00000003358	1 retrocopy	retro_btau_629,
Canis familiaris	ENSCAFG00000032480	1 retrocopy	retro_cfam_797,
Choloepus hoffmanni	ENSCHOG00000003286	6 retrocopies	retro_chof_110, retro_chof_1840, retro_chof_2447, retro_chof_3, retro_chof_41, retro_chof_581,
Felis catus	ENSFCAG00000009220	1 retrocopy	retro_fcat_42 ,
Macropus eugenii	ENSMEUG00000010002	1 retrocopy	retro_meug_2119,
Myotis lucifugus	ENSMLUG00000004210	1 retrocopy	retro_mluc_2396,
Mustela putorius furo	ENSMPUG00000012043	1 retrocopy	retro_mputfur_885,
Sus scrofa	ENSSSCG00000021325	2 retrocopies	retro_sscr_1129, retro_sscr_422,
Ictidomys tridecemlineatus	ENSSTOG00000003692	1 retrocopy	retro_itri_1118,
Vicugna pacos	ENSVPAG00000010692	1 retrocopy	retro_vpac_368,