RetrogeneDB ID: retro_ecab_177

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:87993545..87994574(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: B4GALT4
• Ensembl ID: ENSECAG00000013334
• Aliases: None
• Description: UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4 [Source:HGNC Symbol;Acc:927]

Sequence

>retro_ecab_177
ATGGGCTGCAATGTGACTTTCCACCTTTCTTACAAATTCCGGTTACCGTTGCTTCTTACCTTATGCCTGACGGTGGTTGG
GTGGGCCACCAGGAACTACTTTGTAGCTGCTATTCAAGAGATTCCTAAAGCAAAGGATTTCATGCCTAATTTCAACAACC
CTCTCGTTTTGGAGAAGAAACAAACTCTGACCAATGAAGCATCCACGACAACTGCAAACCTTGACAACTGCCCTTCCATG
TCTCCATACCTCAGAGGCCAGAACAAGCTCTTTTTCAAACCGGATCTCACTCTGGAAGAAGTGCAGGCAGAAAACCCCAA
CGTGCGCAGAGGACACTATCGCCCGAGGAATGCAGGGCTCTGCAGCGGGTCGCCATCCTCATTCCACACCGGAACAGGGA
GAAGCACCTGATGTACCTGCTGGAACACCTTCATCCCTTTTTGCATCGGCAGCAGCTGGAGTACGGCATCTTTGTCATCC
ACCAGGCTGGAAGTAAAAAGTTTAATTGAGCCAAACTCTTGAATGTGGGCTATCTAGAAGCTCTCAAGGATGAAAATTGG
GACTGCTTTATATTCCACGATGTGGATCTGGTGCCGGAGAATGACCTGAACCTTTACAAGTGTGAGGATCAGCCCAAGCA
TCTGGTGGTTGGCAGGAACAGCACTGGATACAGGTTACGTTACAGCGGATATTTTTGGGGGCGTTACTGCCCTAAGCAGA
GAACAATTTTTCGAGGTGAAGGGATTCTCTAACAACTACTGGGGATGGGGAGGCGAAGACGATGACCTCAGACTCAGGGT
TGAGCTTCATAGAATGAAAATAATCCGGCCAATGCCTGAAGTGAGTAAATACACGATGATCTTCCATACCAGAGACCAAG
GCAATGAAGTGAACACAGAGCGGATGAAGCTCTTACATCAAGTGTTACGAGTCTGGAGAACAGATGGGTTGACCAGTTGT
GTTTATAAATTACTCTGTGTGGATTATAATCCTCTGTATATCAACATCACAGTGGATTTCTGGTCTGGC

Alignment

ORF - retro_ecab_177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.91 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGCSVTFHLSYKFRLLLLLTLCLMVVGWATSNYFVAALQEIPKAKDFMANFNNPLVLEKKQTLTNEASTT
          MGC.VTFHLSYKFRL.LLLTLCL.VVGWAT.NYFVAA.QEIPKAKDFM.NFNNPLVLEKKQTLTNEASTT
Retrocopy MGCNVTFHLSYKFRLPLLLTLCLTVVGWATRNYFVAAIQEIPKAKDFMPNFNNPLVLEKKQTLTNEASTT

Parental  TANLDNCPSMSPYLRGQNKLFFKPDLTLEEVQAENPNVRRGRYHP-EECRALQRVAILIPHRNREKHLMY
          TANLDNCPSMSPYLRGQNKLFFKPDLTLEEVQAENPNVRRG.Y.P.EECRALQRVAILIPHRNREKHLMY
Retrocopy TANLDNCPSMSPYLRGQNKLFFKPDLTLEEVQAENPNVRRGHYRP<EECRALQRVAILIPHRNREKHLMY

Parental  LLEHLHPFLQRQQLEYGIYVIHQAGSKKFNRAKLLNVGYLEALKDENWDCFIFHDVDLVPENDLNLYKCE
          LLEHLHPFL.RQQLEYGI.VIHQAGSKKFN.AKLLNVGYLEALKDENWDCFIFHDVDLVPENDLNLYKCE
Retrocopy LLEHLHPFLHRQQLEYGIFVIHQAGSKKFN*AKLLNVGYLEALKDENWDCFIFHDVDLVPENDLNLYKCE

Parental  DQPKHLVVGRNSTGYRLRYSGYF-GGVTALSREQFFKVNGFSNNYWGWGGEDDDLRLRVQLHRMKIIRPM
          DQPKHLVVGRNSTGYRLRYSGYF.GGVTALSREQFF.V.GFSNNYWGWGGEDDDLRLRV.LHRMKIIRPM
Retrocopy DQPKHLVVGRNSTGYRLRYSGYF>GGVTALSREQFFEVKGFSNNYWGWGGEDDDLRLRVELHRMKIIRPM

Parental  PEVGKYTMIFHTRDQGNEVNIERMKLLHQVSRVWRTDGLSSCVYKLLSVDYNPLYINITVDFWSG
          PEV.KYTMIFHTRDQGNEVN.ERMKLLHQV.RVWRTDGL.SCVYKLL.VDYNPLYINITVDFWSG
Retrocopy PEVSKYTMIFHTRDQGNEVNTERMKLLHQVLRVWRTDGLTSCVYKLLCVDYNPLYINITVDFWSG

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	0.06 RPM	19.77 RPM
SRP021940_cerebellum	0.00 RPM	12.83 RPM
SRP021940_embryo	0.13 RPM	30.15 RPM
SRP021940_placental_villous	0.10 RPM	52.97 RPM
SRP021940_synovial_membrane	0.05 RPM	12.02 RPM
SRP021940_testis	0.00 RPM	25.07 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_177 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013334	1 retrocopy	retro_ecab_177 ,
Tupaia belangeri	ENSTBEG00000012268	1 retrocopy	retro_tbel_3287,