RetrogeneDB ID: retro_fcat_1916

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:48940955..48941838(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSFCAG00000025986
• Aliases: None
• Description: cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]

Sequence

>retro_fcat_1916
ACCACTAGATGACTGCTAGAAGTTCAGAAGTTCATAAAGCATGGAGTTAACACTGAAGAAGACTTAGTCCAAGAAGGGGA
GATCACCCTTCTAGGTGGTGTAGGAAAACAGAATGAAAAACTATGAAACTTTACAAAAAGTCCTCACACATTCAGTTGGT
CAGTTTAACAGAAGTGCCTTTACTGGTTGATGTGTCTTGTTTACCGGCTCAGTTACATGACTCAATTCTGAACAAAGTGA
AAGACCTCATTTTCAAGTACAGAACAGTAGCATCTTGCCCACCAGTACAGATAGAAAAACTAATAGAGAAATGTGGAAGC
ATCATTTTTCAGTGGTGTAAGGTCGATGATAACTTTGCCGCTCAAATTACAGTCTTCAGTTCCACAAATGCACTTCAAAT
CATTTTGAGGACATATCTGTAGACTCTGAAACTGAGCTCATAGTATTGCACATAGACCCCAACATTGATTATCAGTTCAG
AGTCTTTGCCTGAAGAGATGGCCAACAGGAGTGGAGTCCTTGGGGCATCCTCCAAATGGGTCACTCTCCATTGGTGCCTC
ATGAGTGCACAGCTGGCTTTGAGGGGTACAGACTGAGGAATTGAAAAAATATAGCCCTCCAGAATGATTGTGAATCCTCA
GATATCCTCTGCTCCAGTGCTCCAACTTATTTCTGTGGGCAGACATTGACATTCAGAGTTAAAACTGAGGATAACCAGAC
AAAGGAGACAGTATAGGAGTGTGTGCAGAAAAATAGAATGGATATGACCCTCTGCAGCATGATCAAGCAGTGTGCATTAT
ACAAATGGTGCAGTTTTGTAAGTGGAAAATAAATGACTGATTAGTTGCTAGCAGATATTGAAGTTGTGACTCTAGGATCC
ACC

Alignment

ORF - retro_fcat_1916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.76 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TIKPLDDCQKLIEHGVHTAEDLVQEGEIAILGGVGEQNEKLWNFTK-KASHIQLDSLPEVPLLVDVPCLS
          T...L...QK.I.HGV.T.EDLVQEGEI..LGGVG.QNEKL.NFTK.K.SHIQL.SL.EVPLLVDV.CL.
Retrocopy TTR*LLEVQKFIKHGVNTEEDLVQEGEITLLGGVGKQNEKL*NFTK<KSSHIQLVSLTEVPLLVDVSCLP

Parental  AQLDDSILNIVKDHIFKHGTVASRPPVQIEELIEKPGGIIVRWCKVDDDFIAQ-DYRLQFRKCTSNHFED
          AQL.DSILN.VKD.IFK..TVAS.PPVQIE.LIEK.G.II..WCKVDD.F.AQ..Y.LQF.KCTSNHFED
Retrocopy AQLHDSILNKVKDLIFKYRTVASCPPVQIEKLIEKCGSIIFQWCKVDDNFAAQ<NYSLQFHKCTSNHFED

Parental  VYVGSETEFIVLHIDPNVDYQFRVCARGDGRQEWSPWSVPQMGHSTLVPHEWTAGFEGYSLSSRRNIALR
          ..V.SETE.IVLHIDPN.DYQFRV.A..DG.QEWSPW...QMGHS.LVPHE.TAGFEGY.L....NIAL.
Retrocopy ISVDSETELIVLHIDPNIDYQFRVFA*RDGQQEWSPWGILQMGHSPLVPHECTAGFEGYRLRN*KNIALQ

Parental  NDSESSGVLYSSAPTYFCGQTLTFRVETV-GQPDRRDSIGVCAEKQNGYDSLQRDQAVCI-STNGAV-FV
          ND.ESS..L.SSAPTYFCGQTLTFRV.T..G.PD..DSIGVCAEK.NGYD.LQ.DQAVCI..TNGAV.FV
Retrocopy NDCESSDILCSSAPTYFCGQTLTFRVKTE<G*PDKGDSIGVCAEK*NGYDPLQHDQAVCI<YTNGAV<FV

Parental  NGKEMTN----QLPAVTSGST
          .GK.MT.........VT.GST
Retrocopy SGK*MTD*LLADIEVVTLGST

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	30.53 RPM
SRP017611_kidney	0.00 RPM	9.07 RPM
SRP017611_liver	0.00 RPM	5.56 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1916 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1916 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
Echinops telfairi	ENSETEG00000017897	1 retrocopy	retro_etel_313,
Felis catus	ENSFCAG00000025986	1 retrocopy	retro_fcat_1916 ,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Ictidomys tridecemlineatus	ENSSTOG00000012342	1 retrocopy	retro_itri_1384,