RetrogeneDB ID: retro_fcat_1860

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:66234474..66234872(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN3
• Ensembl ID: ENSFCAG00000025746
• Aliases: None
• Description: tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

Sequence

>retro_fcat_1860
GAAAGTGTATATAAGGCCTACAGTGGAACCAACCCCAGTGACACTAGCCCGGCTGCTCATCACGTACAGAGATAGCTGCA
CTCTTGTGGAATTCACAACTATTCAGACTGGGACAATCCAGACCGGTTCAAGGAAACCAAAAACCAGAGTGTCCCTCTTA
GCTGTGCAGAGAGACCACCAGCAGCTCCAACGGTCTGGCCCACCGCTCCGACCTCCACGCTGAGGGATGTGAGGCTCTGG
TTGTGAAGGAGCTACGAGAAATCATGATGCGTATCATCTGGGTCGTGCGGGCATTTGCAGCTATTCAGCTGCTGGGCGTG
CTGTGTGCATGCATCAGATTGTGCAGGACGAGTAGAGATCCTGCTTCTGAGCCCTCCATCACCGGCGAAACCTCTGCC

Alignment

ORF - retro_fcat_1860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 57.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKVYKTYNGTNPDAASRAIDYVQRQLHCCGIHNYSDWENTDWFKETKNQSVPLSC-CRETASSCNGSLAH
          ..VYK.Y.GTNP...S.A...VQR.LH.CGIHNYSDW.N.D.FKETKNQSVPLSC.CRET.SS.NG.LAH
Retrocopy ESVYKAYSGTNPSDTSPAAHHVQR*LHSCGIHNYSDWDNPDRFKETKNQSVPLSC<CRETTSSSNG-LAH

Parental  PSDLYAEGCEALVVKKLQEIMMHVIWAALAFAAIQLLGMLCACIVLCRRSRDPAYELLITGGTYA
          .SDL.AEGCEALVVK.L.EIMM..IW...AFAAIQLLG.LCACI.LCR.SRDPA.E..ITG.T.A
Retrocopy RSDLHAEGCEALVVKELREIMMRIIWVVRAFAAIQLLGVLCACIRLCRTSRDPASEPSITGETSA

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	213.48 RPM
SRP017611_kidney	0.00 RPM	149.95 RPM
SRP017611_liver	0.00 RPM	22.85 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1860 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1860 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089, retro_btau_1650,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860 ,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268,