RetrogeneDB ID: retro_ecab_1091

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:111508787..111509369(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16orf72
• Ensembl ID: ENSECAG00000009430
• Aliases: None
• Description: chromosome 16 open reading frame 72 [Source:HGNC Symbol;Acc:30103]

Sequence

>retro_ecab_1091
ATGTGGGGACCCCTTCCCACGAAGTGCGGCATGGCCGTGACCAGCCTCTACAAAGAGAGCGGGGATGCCCACCAGCGAAG
TTTTGACCTGGGCGTCCAGGTGGGCTACCAGCGTCGCATCAGAGACGTGCTGGAGTGGGTGAAGAAGGGCCGGAGCACCA
TTCTCCGTGAAGACCTGATTAGCTTCCTGTGTGGCAAAGTGCCGCCCGTGCCGCCACCACGCTCCCCCAGGACGCCCTCG
AAGCCCCCCGCTGGGGCCACCAGCCAGGCCGCAGCCATCGAATCCAGCTCGTCGGTGGAGGTCGACTTGCAGCCCTTCCA
TGAGGCCATCGCGCTGCATGGCCTCAGTGGCGCCATGGCCAGCATCAGCGTGCGGTCGGGCACACCTGGCTCCCCACCTC
AGGCCAGTGGCGGCGCCAGCGGTGGGCGTCAAAAAAGTAATGGCCTTGAAGACGACTTGAAGCCCTTCGACCTGGAAGAA
CTGGCCCCCCATGCAGACAGTGGGGGGAACCGCAAGCGCACCTCGGCCCAGTGTGGGGATGGCATCTCAGACTCCCCAAC
CCACAAGCGCAACCGAATGGTC

Alignment

ORF - retro_ecab_1091 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.13 %
• Parental protein coverage: 94.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LWVPIQN-AATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIRREDLISFLCGK---V
          .W.P.......AVT.LYKES.D.HQRSFD.G.Q.GYQRR..DVL.WVKK.R.TI.REDLISFLCGK...V
Retrocopy MWGPLPTKCGMAVTSLYKESGDAHQRSFDLGVQVGYQRRIRDVLEWVKKGRSTILREDLISFLCGKVPPV

Parental  PPPRNSRAPPRLTVVSPSRATSAETSSSVETDLQPFREAIALHGLSGAMASISVRSSTPGSPTHVSSGSN
          PPPR..R.P........S.A...E.SSSVE.DLQPF.EAIALHGLSGAMASISVRS.TPGSP...S.G..
Retrocopy PPPRSPRTPSKPPAGATSQAAAIESSSSVEVDLQPFHEAIALHGLSGAMASISVRSGTPGSPPQASGGAS

Parental  ASRRR-NGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
          ..R...NGL.D.DL..F..EE.A.H.D.GG.RKRTSAQCGD.I.DSPTHKRNRM.
Retrocopy GGRQKSNGLED-DLKPFDLEELAPHADSGGNRKRTSAQCGDGISDSPTHKRNRMV

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	0.24 RPM	25.38 RPM
SRP021940_cerebellum	1.82 RPM	26.07 RPM
SRP021940_embryo	2.71 RPM	30.84 RPM
SRP021940_placental_villous	0.24 RPM	27.23 RPM
SRP021940_synovial_membrane	0.16 RPM	21.44 RPM
SRP021940_testis	2.94 RPM	46.68 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1091 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1091 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4765
Pan troglodytes	retro_ptro_3172
Gorilla gorilla	retro_ggor_2968
Pongo abelii	retro_pabe_163
Mus musculus	retro_mmus_3460
Rattus norvegicus	retro_rnor_156
Sus scrofa	retro_sscr_1177
Canis familiaris	retro_cfam_147

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091 ,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,