RetrogeneDB ID: retro_ecab_1049

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un1813:3896..5012(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXL3
• Ensembl ID: ENSECAG00000011128
• Aliases: None
• Description: F-box and leucine-rich repeat protein 3 [Source:HGNC Symbol;Acc:13599]

Sequence

>retro_ecab_1049
GATCAGGCCCGCGCATTTTCTGTATGTAGGAGATGGAACGAAGTTTTTCATATCCCTGACCTTTGGAGAAAGTTTGAATT
TGAACTGAACCAATCAGCAACTTTGTCTTTTCAAGCCACTCCTCGTGATCTCATTCAGCAGATCTTTAAAAGGCATGTTG
CCTGTCTCCAGTATGTCAGCTTTAAGGTTGATAGCAGTACTGAATCAGCAGAGGCTGCCTGCGATATATTTTCTCAGCTG
GGAAATGGTTCTCCACACCTTGGGCTTGATTTCTAGGGCCAATCCAAGTTTTATGAACGTGTCAAAGTCTCATTTTGTGT
CAGCACTTACACTTGCTTGTGTCAACTCAAAATCATTATCATCAATCAAACTTGAAGACCCACCCATGGATGACCCTTCA
CTGAAGGTTCTGGTGGCCAATAATAGTGATACTCTAACACTCCTAAAAATGAGCAGCTGTCCTTATGTTTCATCTGATGG
AATCCTTTGTGTAGCTGATCATTGTCAAGGCCTTAGAGAACTGGCATTGAATTATTACATTCCAAGTGATGAACTTCTGG
CCCTTTCAAGTGAGACTCATGTTAACCTTGAACATCTTCGAATTGATGTTGTGAGTGAAAATCCTGGACAAAGTAAATTT
CATTCCATTAAAAAACAAAGTTGAGATGCACTTATTAAACACTCCCCTGGAGTTAATGTTGTCATATACTTCTTTTTAAA
CGAAGAGGAATTTGTGACATTCTTCACAGAAGAATCCCCTGTCACTCATCTTTATTTCGGTCGGTCAGTAAGCAAAGCGG
TCCTAAGACGGATAGGTCCTATCTGCCCACGCCTAGTTGAGTTAGTGGTGTGTGCAAACGGTCTTCAGACTCTTGACAAT
GAGCTGATCTGTATTGCTCAACACTGTAAAAACTGAACAGCCTTGGGCCTCAGTGCATGTGAAGTTTGCTGCAGTGCCGT
GGTTGAGTTTGTAAGGCTGGGTGGGAGGAGGCTCGCGCAGCTCTCTGTGATGGAGGAGGTTCTGACCCGGATGGGGATTA
CGGCCTGGATAAAATTCACGCTGAAGCCTCCAAATACCTGGGAAGAACGTGGTTCCCGGATGTCATGCCTGGCTGG

Alignment

ORF - retro_ecab_1049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.74 %
• Parental protein coverage: 87.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DRAHASQVCRSWNQVFHMPDLWRCFEFELNQPATSYLKATHPELIKQIIKRHSNHLQYVSFKVDSSKESA
          D.A.A..VCR.WN.VFH.PDLWR.FEFELNQ.AT....AT...LI.QI.KRH...LQYVSFKVDSS.ESA
Retrocopy DQARAFSVCRRWNEVFHIPDLWRKFEFELNQSATLSFQATPRDLIQQIFKRHVACLQYVSFKVDSSTESA

Parental  EAACDILSQLVNCSLKTLGL-ISTARPSFMDLPKSHFISALTVVFVNSKSLSSLKIDDTPVDDPSLKVLV
          EAACDI.SQL.N.S...LGL.IS.A.PSFM...KSHF.SALT...VNSKSLSS.K..D.P.DDPSLKVLV
Retrocopy EAACDIFSQLGNGS-PHLGL>ISRANPSFMNVSKSHFVSALTLACVNSKSLSSIKLEDPPMDDPSLKVLV

Parental  ANNSDTLKLLKMSSCPHVSPAGILCVADQCHGLRELALNYHLLSDELLLALSSEKHVRLEHLRIDVVSEN
          ANNSDTL.LLKMSSCP.VS..GILCVAD.C.GLRELALNY...SDE.LLALSSE.HV.LEHLRIDVVSEN
Retrocopy ANNSDTLTLLKMSSCPYVSSDGILCVADHCQGLRELALNYYIPSDE-LLALSSETHVNLEHLRIDVVSEN

Parental  PGQTHFHTIQKSSWDAFIRHSPKVNLVMYFFLYEEEFDPFFRYEIPATHLYFGRSVSKDVLGRVGMTCPR
          PGQ..FH.I.K.S.DA.I.HSP.VN.V.YFFL.EEEF..FF..E.P.THLYFGRSVSK.VL.R.G..CPR
Retrocopy PGQSKFHSIKKQS*DALIKHSPGVNVVIYFFLNEEEFVTFFTEESPVTHLYFGRSVSKAVLRRIGPICPR

Parental  LVELVVCANGLRPLDEELIRIAERCKNLSAIGLGECEVSCSAFVEFVKMCGGRLSQLSIMEEVLI-PDQK
          LVELVVCANGL..LD.ELI.IA..CKN..A.GL..CEV.CSA.VEFV...G.RL.QLS.MEEVL..PD..
Retrocopy LVELVVCANGLQTLDNELICIAQHCKN*TALGLSACEVCCSAVVEFVRLGGRRLAQLSVMEEVLT<PDGD

Parental  YSLEQIHWEVSKHLGRVWFPDMMPTW
          Y.L..IH.E.SK.LGR.WFPD.MP.W
Retrocopy YGLDKIHAEASKYLGRTWFPDVMPGW

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
SRP021940_articular_cartilage	0.00 RPM	29.22 RPM
SRP021940_cerebellum	0.00 RPM	21.45 RPM
SRP021940_embryo	0.00 RPM	13.48 RPM
SRP021940_placental_villous	0.00 RPM	16.45 RPM
SRP021940_synovial_membrane	0.00 RPM	14.71 RPM
SRP021940_testis	0.00 RPM	24.87 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1049 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1049 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1049 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011128	3 retrocopies	retro_ecab_1048, retro_ecab_1049 , retro_ecab_1124,
Otolemur garnettii	ENSOGAG00000000250	1 retrocopy	retro_ogar_2765,