RetrogeneDB ID: retro_ecab_1122

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:82113699..82114035(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MIF
• Ensembl ID: ENSECAG00000012792
• Aliases: None
• Description: macrophage migration inhibitory factor (glycosylation-inhibiting factor) [Source:HGNC Symbol;Acc:7097]

Sequence

>retro_ecab_1122
ATGCCAATGGTGGCGGTGGACACCCACGTGCCCCGCGTCTCCGTGCTGGATGAGTTCCTCTGCGAGTTCACCCAGCAGCT
GGTGCAGGCCATAGGCAAGCCGGCACGGTCCATCACGGTGCGTGTGGTCCGGGCCAGATCATGGCCTTCGGCGGCTTGAG
CGCCGTGCGCGCCCTGCACCCTGCATAAGCATCAGCAAGATCCGAGATGCTCCAGACCGCTCCTTCAGCAAGCTGCTGTA
CGGCCGGCTGGCCGAGTACCTGCGTGTCAGCCCAAAAGGATCTACATCCAATACTACGACATAAATTCAGCCAATATGGG
CTAGAACGGCTCTACC

Alignment

ORF - retro_ecab_1122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.07 %
• Parental protein coverage: 98.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPMFVVNTNVPRASVPDGLLSELTQQLVQATGKPAQYIAVHVV-PDQLMTFGGSSEPCAL-CSLHSIGKI
          MPM..V.T.VPR.SV.D..L.E.TQQLVQA.GKPA..I.V.VV.P.Q.M.FGG.S...AL.....SI.KI
Retrocopy MPMVAVDTHVPRVSVLDEFLCEFTQQLVQAIGKPARSITVRVV<PGQIMAFGGLSAVRAL<APCISISKI

Parental  GGAQNRSYSKLLCGLLAERLRVS-PDRIYINYYDMNAANVGWNGST
          ..A..RS.SKLL.G.LAE.LRVS.P.RIYI.YYD.N.AN.G.NGST
Retrocopy RDAPDRSFSKLLYGRLAEYLRVS<PKRIYIQYYDINSANMG*NGST

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	207.37 RPM
SRP021940_cerebellum	0.00 RPM	140.53 RPM
SRP021940_embryo	0.00 RPM	166.32 RPM
SRP021940_placental_villous	0.00 RPM	131.49 RPM
SRP021940_synovial_membrane	0.00 RPM	90.89 RPM
SRP021940_testis	0.00 RPM	83.45 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1122 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1122 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010668	3 retrocopies	retro_cjac_2903, retro_cjac_3132, retro_cjac_357,
Cavia porcellus	ENSCPOG00000013520	1 retrocopy	retro_cpor_879,
Dasypus novemcinctus	ENSDNOG00000014555	1 retrocopy	retro_dnov_36,
Equus caballus	ENSECAG00000012792	1 retrocopy	retro_ecab_1122 ,
Echinops telfairi	ENSETEG00000012052	3 retrocopies	retro_etel_2001, retro_etel_2046, retro_etel_509,
Mus musculus	ENSMUSG00000033307	8 retrocopies	retro_mmus_1573, retro_mmus_1759, retro_mmus_1878, retro_mmus_2182, retro_mmus_2444, retro_mmus_3016, retro_mmus_3315, retro_mmus_489,
Ochotona princeps	ENSOPRG00000012184	1 retrocopy	retro_opri_968,
Rattus norvegicus	ENSRNOG00000006589	6 retrocopies	retro_rnor_137, retro_rnor_1608, retro_rnor_1644, retro_rnor_2263, retro_rnor_31, retro_rnor_361,