RetrogeneDB ID: retro_ecab_450

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:55206524..55207232(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUCA1
• Ensembl ID: ENSECAG00000024652
• Aliases: None
• Description: fucosidase, alpha-L- 1, tissue [Source:HGNC Symbol;Acc:4006]

Sequence

>retro_ecab_450
GTTGATGAGTTGGGAACAGCTGTTCAGAAGAGGAACATATGCTATGGACTCTATCATTCATTCTTAGAATGGTTCCATCC
ACTCTACCTACTTGATAAGAAAAATGGCTTTGAAACATAGCATTTTGTCAGTGTGAACACAATGCCAGAGTTATATGACA
TTGTTAACAGGTACAAATCTGACCTGATTTGGTCTAATGGAGAGTGGAAATGTCCTGATACTTAGCAGAAGTCTACAAAT
TTTCTTTCTTGGCTTTACAATGATAGCTCTGTCAAGGATGAGGTGGTAGTAAATGACTAATGGGACCAGAAATGTTCCTG
TTACCCTGGAGGATACTACAACTGTCAAGATAAATGCAAGCCAGAGAGGTTGCTAGATCACAAGTTGGAGACATGTACCA
CTGTTGACAAGTCATCCTGGGGCTATCATGGGGACATGGCCATGCCTGACATTGCAAATGAATCTGAAATCATTTCAGAA
CTCGTTCAGACAGTAAGTTTGGGAGGTAACTATCTTCTTAACATTGAACCAACTAAAGATGGACTGATTGTTCCCATCTT
CCAAGAAAGGCTTTTTGCTGTTGGGAAACGGCTGAACATCACTGGGGAGGTTATTTATGCATCTAAACCATCAAGGGTAC
AATCAGAGAAGAATGTGATATCTATATGGTATATCTCAAAAGGATCAGGAGTCTTAACCTTCAGTCTC

Alignment

ORF - retro_ecab_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.88 %
• Parental protein coverage: 53.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGELGAAIRKRNIRYGLYHSLLEWFHPLYLLDKKNGFKTQHFVSAKTMPELYDLVNRYKPDLIWSDGDWE
          V.ELG.A..KRNI.YGLYHS.LEWFHPLYLLDKKNGF.T.HFVS..TMPELYD.VNRYK.DLIWS.G.W.
Retrocopy VDELGTAVQKRNICYGLYHSFLEWFHPLYLLDKKNGFET*HFVSVNTMPELYDIVNRYKSDLIWSNGEWK

Parental  SPDTYWNATYFLSWLYNDSPVKDVVVVNDRWGQNCSCHHGGYYNCQDKFKPKSLPDHKWEMCTSIDKYSW
          .PDT....T.FLSWLYNDS.VKD.VVVND.W.Q.CSC..GGYYNCQDK.KP..L.DHK.E.CT..DK.SW
Retrocopy CPDT*QKSTNFLSWLYNDSSVKDEVVVND*WDQKCSCYPGGYYNCQDKCKPERLLDHKLETCTTVDKSSW

Parental  GYRRDMVMSDITTEFEIISELIQTVSLGGNYLLNVGPTKDGLIVPIFQERLLAVGKWLSINGEAIYASKP
          GY..DM.M.DI..E.EIISEL.QTVSLGGNYLLN..PTKDGLIVPIFQERL.AVGK.L.I.GE.IYASKP
Retrocopy GYHGDMAMPDIANESEIISELVQTVSLGGNYLLNIEPTKDGLIVPIFQERLFAVGKRLNITGEVIYASKP

Parental  WRVQLENNMTSVWYTSKGSTVYAIFL
          .RVQ.E.N..S.WY.SKGS.V....L
Retrocopy SRVQSEKNVISIWYISKGSGVLTFSL

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	32.35 RPM
SRP021940_cerebellum	0.00 RPM	21.19 RPM
SRP021940_embryo	0.03 RPM	24.73 RPM
SRP021940_placental_villous	0.00 RPM	168.05 RPM
SRP021940_synovial_membrane	0.00 RPM	46.56 RPM
SRP021940_testis	0.00 RPM	23.40 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_450 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_450 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012304	2 retrocopies	retro_chof_1090, retro_chof_542,
Equus caballus	ENSECAG00000024652	1 retrocopy	retro_ecab_450 ,
Loxodonta africana	ENSLAFG00000015305	1 retrocopy	retro_lafr_252,
Microcebus murinus	ENSMICG00000007213	1 retrocopy	retro_mmur_542,
Tupaia belangeri	ENSTBEG00000013160	1 retrocopy	retro_tbel_3390,