RetrogeneDB ID: retro_fcat_470

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:57009662..57010462(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC17
• Ensembl ID: ENSFCAG00000009938
• Aliases: None
• Description: leucine rich repeat containing 17 [Source:HGNC Symbol;Acc:16895]

Sequence

>retro_fcat_470
GACAACCCGTGGCATGTACTCATGAGATGGAAATGCTTATTTCAATGTTGCGGATTCCAAGAAACCCGGATTTGGGGAAC
TACACCAAGTGTGAAAGCCCACAAGATCTAAAAATCAAAAACTGCTGCAGATAAACCTTGAACAGTTATGAAATGAAGAA
GAAAGGGAACAATTAGACCTGAAACCCCAATGTCAGGGAGACCCCCAGTCATCAAGCCTGAGGTAGACTCTTCTCTTTGC
TCCAATTACATGTTTCCCATACAAACGTTGGACTGCAAACAGAAAGAGTAGAAGAAAGTTCCAAACAACATCCCTCCAGA
CATTGTTAAACTTGACTTGTCATACAATGAAATCAACCAGCTTTGATCCAAGGAGTTTGAAGATATTCGTGAGCTAAAAA
AATTAAACCTCAGCAGCAATGGTATTGAATTCATAGATACTGGTGCTTTTTTAGGATTCACACATTTAGAAGAGTTAGAA
TTATCAAACAAAAGTCTACAAAACTATGATTGTGGTGTATTAGAAGACTTGTATTTTTTGCAACTCTTGTGGATCAGAGA
TACCCTTGGAAATGTGACTACAATATCCACTACCTCTACTACTGGTTAAAGCACCACTACAACGTACAATATAATGGCCT
GGGATGCAAGATGGCTGAAGAATACACAGGGTGGTTTGTGGGAAAATATGTTCACAGTTACTTTGAAGAATGCCCCAAAG
ACAAATTACACCCTGAGACATTTGATCAAGGTCAAGAAGATGATGACTGGGAGAAGATTCATAGGGATCATGTAGCAGAG

Alignment

ORF - retro_fcat_470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.02 %
• Parental protein coverage: 61.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DNPWH-CTCEMETLISMLQIPRNRNLGNYAKCERPQDLK-NKKLRQIKSEQLCNEEEREQLDPKPQ-VSG
          DNPWH.CT.EME.LISML.IPRN..LGNY.KCE.PQDLK.N.KL.QI..EQL.NEEEREQLD.KPQ..SG
Retrocopy DNPWH<CTHEMEMLISMLRIPRNPDLGNYTKCESPQDLK<NQKLLQINLEQL*NEEEREQLDLKPQ<MSG

Parental  RPPVIKPEVDSTLCYNYVFPIQTLDCKRKELKKVPNNIPPDIVKLDLSYNKINQLRPKEFEDVHELKKLN
          RPPVIKPEVDS.LC.NY.FPIQTLDCK.KE.KKVPNNIPPDIVKLDLSYN.INQL..KEFED..ELKKLN
Retrocopy RPPVIKPEVDSSLCSNYMFPIQTLDCKQKE*KKVPNNIPPDIVKLDLSYNEINQL*SKEFEDIRELKKLN

Parental  LSSNGIEFIDPAAFLGLTHLEELDLSNNSLQNFDYGVLEDLYFLKLLWLRDN-PWRCDYNIHYLYYWLKH
          LSSNGIEFID..AFLG.THLEEL.LSN.SLQN.D.GVLEDLYFL.LLW.RD..PW.CDYNIHYLYYWLKH
Retrocopy LSSNGIEFIDTGAFLGFTHLEELELSNKSLQNYDCGVLEDLYFLQLLWIRDT<PWKCDYNIHYLYYWLKH

Parental  HYNVHYNGLECKMPEEYKGWFVGKYVRSYFEECPKDKLPAYPETFDQDPEDDEWEKIHRDHTAK
          HYNV.YNGL.CKM.EEY.GWFVGKYV.SYFEECPKDKL...PETFDQ..EDD.WEKIHRDH.A.
Retrocopy HYNVQYNGLGCKMAEEYTGWFVGKYVHSYFEECPKDKL--HPETFDQGQEDDDWEKIHRDHVAE

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	0.80 RPM
SRP017611_kidney	0.00 RPM	1.44 RPM
SRP017611_liver	0.00 RPM	0.30 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_470 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_470 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013916	1 retrocopy	retro_chof_1900,
Felis catus	ENSFCAG00000009938	1 retrocopy	retro_fcat_470 ,