RetrogeneDB ID: retro_fcat_1910

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:41516926..41517701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH12
• Ensembl ID: ENSFCAG00000014092
• Aliases: None
• Description: retinol dehydrogenase 12 (all-trans/9-cis/11-cis) [Source:HGNC Symbol;Acc:19977]

Sequence

>retro_fcat_1910
AGACAGCTTGGTAGCAGAGGAGCCCAACTATGCATTGCCTACCAGGATATACTTAAGGGGGATAATCTGCTGGCCAGTGA
AATCTAGGCCAATACAAAGAACTCTCAGATGCTAATTCAGAAACTGGACCCGTCCAATACCAAATCCACCTGAGCCTTTG
CTAAGGGCTTTCTGGCAGAGAAAAAACAGCTCCATATTTTGACCAACAAAGCAAGAGTGATAATGCATCCATATTCCAAG
ACAGCTGGTGACTTTGAAACCCACCTAGGAGTCAACCACCTGGGCCACTTCTTTTGTGCCCACTTTCTCCTGGAGCTGCT
GAAAACATCTGCACCCTCACAGGTGATGAACCTGTCATCAGTAACTCACCATGCTGGCAAGATTCATTTCCACAAACTCT
AGGGTAAGAAGCACTACAGCCAGGAGTTTTGCTCATTGCCACAGCTAGGTGGCCAATATATTTTTAATTGGGAACTGGCC
AAGAGGCTCCAAGGCACAGGGGTCACCACCTATGCAGTGCACCCAGGCATCATCTACTCCCAACTGGTCTAGCACTACTT
CTTGTTGTGCCTGCTCTGGAGGGTCTTCTCCCACTTCATCAAGTCAACATGGTAGGGGGCACAGACCAGCCTCCACTGTG
CCTTGGTTGAGAGCCTGGAGCCCTAGTGTGACAAGTACCTCAGTGACTGCAGGAGGACCTGGGTGCCCCAAGGGTCTGAA
ATAGCAAAACCATTGAGTGCCTGTAGAATGTCACTGTGAGCTTCTAAAAATCCAG

Alignment

ORF - retro_fcat_1910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.78 %
• Parental protein coverage: 80.62 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RELARRGARVYIACRDVLKGESA-ASEIRADTKNSQVLVRKLDLSDTKSIRAFAEGFLAEEKQLHILINN
          R.L..RGA...IA..D.LKG....ASEI.A.TKNSQ.L..KLD.S.TKS..AFA.GFLAE.KQLHIL.N.
Retrocopy RQLGSRGAQLCIAYQDILKGDNLLASEI*ANTKNSQMLIQKLDPSNTKST*AFAKGFLAEKKQLHILTNK

Parental  AGVMMCPYSKTADGFETHLGVNHLGHFLLTHLLLERLKESTPSRVVNLSSVVHHAGKIRFHDLQGEKRYS
          A.V.M.PYSKTA..FETHLGVNHLGHF...H.LLE.LK.S.PS.V.NLSSV.HHAGKI.FH.L.G.K.YS
Retrocopy ARVIMHPYSKTAGDFETHLGVNHLGHFFCAHFLLELLKTSAPSQVMNLSSVTHHAGKIHFHKL*GKKHYS

Parental  -RGFAYCHSKLANV-LFTRELARRLQGTGVTTYAVHPGVVSSELIRHSFLLCLLWRIFSPFVKSAREGAQ
          .R.FA.CHS..AN...F..ELA.RLQGTGVTTYAVHPG...S.L..H.FLLCLLWR.FS.F.KS...GAQ
Retrocopy >RSFAHCHS*VANI<IFNWELAKRLQGTGVTTYAVHPGIIYSQLV*HYFLLCLLWRVFSHFIKSTW*GAQ

Parental  TSLHCALAEGLEPLSGKYFSDCKRTWV-SPRARDNETAERLWNVS-CELLGIQ
          TSLHCAL.E.LEP...KY.SDC.RTWV..PR.....T.E.L.NV..CELL.IQ
Retrocopy TSLHCALVESLEP*CDKYLSDCRRTWV<APRV*NSKTIECL*NVT<CELLKIQ

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	0.69 RPM
SRP017611_kidney	0.00 RPM	1.03 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1910 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1910 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673,
Canis familiaris	ENSCAFG00000016446	1 retrocopy	retro_cfam_2068,
Felis catus	ENSFCAG00000014092	1 retrocopy	retro_fcat_1910 ,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,