RetrogeneDB ID: retro_fcat_1342

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:52110422..52111030(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHL3
• Ensembl ID: ENSFCAG00000007237
• Aliases: None
• Description: four and a half LIM domains 3 [Source:HGNC Symbol;Acc:3704]

Sequence

>retro_fcat_1342
CAGAGCTTCTCTTGCCAGTACAGTGAGCTGCTGTGCATTGACTGCTGCAGCAGTGCCTTGTCCCGGGAGTTCACCTGCAG
GGTACGCCATCATGCGTAGGTCCCGGAAGCTGGAATGCAGAAGAGGCCAGACAGGGCCCAAGCACTGCTTCTGGTGCAGT
GGTTTGTGAGCAGCTGCTGGGCTCCTGTTCCTCTGTGCCCTGCAAGCATGCTCATTACTGCGTGCCTTGCCAGGAGAACA
AGCTTTCTCCTCACCGTACCCTCCGCAGCCAGTCATTGACATAGGGTGCATAACATACCGTGATCAGCCCTGGCATCAAG
AATGCCTGGTCTGCACAGGGAGCCAAATGCGCATGGCAGAGCAGCAGTTTGCTTCCAGGGATGATGATCCCTACTGAGTG
GCTGGTTTTGGAGAAGTGTTTGCACCCAAGTGCAGCAGCTGCAAATGTAGCATCATAGGACTGGATGGAGGCAAGTATGT
GCCCTTCTAAGACCACCACTGGCACCACAGCTCCATCTCCTGTGCCCGCTATGCCACCTCCCTGGTGGGCCAAGGATTTG
TGGGGGGCTGAAGACCAAGTGCTGTGCCAGGGGTGCAGCCTGTCAGGC

Alignment

ORF - retro_fcat_1342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.25 %
• Parental protein coverage: 71.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EPFTCQDGELLCNDCYCSAFSSQCSAC-GEPVMPGSRKLEYG-GQTWHEHCFLCSG-CEQPLGSRSFVPD
          ..F.CQ..ELLC.DC.CS...S....C.G...M..SRKLE...GQT...HCF.CSG.CEQ.LGS.S.VP.
Retrocopy QSFSCQYSELLCIDC-CSSALSREFTC>GYAIMRRSRKLECRRGQTGPKHCFWCSG>CEQLLGSCSSVPC

Parental  KGAHYCVPCYENKFAPRCARCSKTLTQGG-VTYRDQPWHRECLVCTGCQTPLAGQQFTSRDDDPYCVACF
          K.AHYCVPC.ENK..P.....S..LT.G...TYRDQPWH.ECLVCTG.Q...A.QQF.SRDDDPY.VA.F
Retrocopy KHAHYCVPCQENKLSPHRTLRSQSLT*GA<ITYRDQPWHQECLVCTGSQMRMAEQQFASRDDDPY*VAGF

Parental  GELFAPKCSSCKRPITGLGGGKYVSFEDRHWHHSCFSCARCSTSLVGQGFVPD-GDQVLCQGCSQAG
          GE.FAPKCSSCK..I.GL.GGKYV.F.D.HWHHS..SCAR..TSLVGQGFV....DQVLCQGCS..G
Retrocopy GEVFAPKCSSCKCSIIGLDGGKYVPF*DHHWHHSSISCARYATSLVGQGFVGG>EDQVLCQGCSLSG

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	1.72 RPM
SRP017611_kidney	0.00 RPM	2.27 RPM
SRP017611_liver	0.00 RPM	1.72 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1342 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1342 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
Felis catus	ENSFCAG00000007237	1 retrocopy	retro_fcat_1342 ,
Mustela putorius furo	ENSMPUG00000014497	1 retrocopy	retro_mputfur_1202,