RetrogeneDB ID: retro_fcat_240

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:89848419..89848854(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000003842
• Aliases: None
• Description: None

Sequence

>retro_fcat_240
GATTTCATAAATCCACTACATAGATATTATCTGTCATTCATGGTACACACCTATGAATTAGAGGAACATGAAATGGAAAC
ATGGAGGCAGTTTATTTACAAGAAACATTGACCTTCAGTGAATACAGCTCTAGATGCAAGCCTCTTTCATGCTGTATATT
TGTTGATTAAAAATGAAAATCCACACATTGCAAGTTGTTGATCCTCTAAGTGGGAATGCTCTTCCTATGCTTACCCACAA
ATGGATTCTCAAGTTCCTCAGGTTTGAATGTCTGATATACCAAAGCCTGCCTTTGTGAAGCAGGACCCAGATGCTCTTGC
ACTTGGGACCCACCACAACATCACCTTCATCCACCCGGACACTCCCTTCAGTAGAGACTTAAACATCTGTGTAGAAAAAC
AAGTATCAGTCTTGTCTATATTGCATGAGTCAGGG

Alignment

ORF - retro_fcat_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.51 %
• Parental protein coverage: 64.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DFINILHRYYKSPMVQIYELEEHKIETWRELYLQETFKPLVNISPDASLFDAVYSLIKN-KIHRLPVIDP
          DFIN.LHRYY.S.MV..YELEEH..ETWR.........P.VN...DASLF.AVY.LIKN.KIH.L.V.DP
Retrocopy DFINPLHRYYLSFMVHTYELEEHEMETWRQ-FIYKKH*PSVNTALDASLFHAVYLLIKN>KIHTLQVVDP

Parental  ISGNALYILTHKRILKFL-QLFMSDMPKPAFMKQNLDALGIGTYHNIAFIHPDTPIIKALNVFVERRVSA
          .SGNAL..LTHK.ILKFL.Q..MSD.PKPAF.KQ..DAL..GT.HNI.FIHPDTP....LN..VE..VS.
Retrocopy LSGNALPMLTHKWILKFL<QV*MSDIPKPAFVKQDPDALALGTHHNITFIHPDTPFSRDLNICVEKQVSV

Parental  LPVVDESG
          L....ESG
Retrocopy LSILHESG

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	16.53 RPM
SRP017611_kidney	0.00 RPM	6.29 RPM
SRP017611_liver	0.00 RPM	8.79 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_240 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_240 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013406	1 retrocopy	retro_amel_1890,
Felis catus	ENSFCAG00000000091	1 retrocopy	retro_fcat_1730,
Felis catus	ENSFCAG00000003842	2 retrocopies	retro_fcat_237, retro_fcat_240 ,
Otolemur garnettii	ENSOGAG00000008645	1 retrocopy	retro_ogar_201,