RetrogeneDB ID: retro_ecab_286

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:17703868..17704363(-)
• Located in intron of: ENSECAG00000011060

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAZAP2
• Ensembl ID: ENSECAG00000007313
• Aliases: None
• Description: DAZ associated protein 2 [Source:HGNC Symbol;Acc:2684]

Sequence

>retro_ecab_286
ATGAACAGCAAAGGTCAATGTCTAACACAGCCAGCCTACCCTGTGCAGCCTCCTGGGAATCCACTGTACCCTTAACCTTG
CATCTTTCTCAGGTTCCACCCCATACTGATGCTCCATCTGCCTACTCAGAGCTCTGTCATCTGAGCTCTGCGTGCACCCG
GGGGCTGCCACAGTCCCCACCATGTCAGCCGCTTTTCTTTGCCCTCACTGTATCTTCCCATGGCCCAGTAAGTGGCTATT
GGTCCTTTAGGTTCCACAATCCCCATGGCTTATTATCTCATCTATCCATCTGGTTCTATTGTGCTGGTAGAAGGAGGGTA
TGATATAGGTGCTAGATTTGGAGCTGGGGCTACTGCTGGCAGTGTTCCTCCTCTACTCCCAGGATGCCCTCCCAAAGCTG
CTCAGCTTGCAGTCATGCAAGGAACCAGTGTCGTTGTAACTCAGTCAAAGGGAAACTTCTTCATGGGTGGCTCAGGAGGT
GACCACACCATCTGG

Alignment

ORF - retro_ecab_286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNSKGQYPTQPTYPVQPPGNPVY-PQALHLPQAPPYTDAPPAYSELYRPSFV-HPGAATVPTMSAAFPGA
          MNSKGQ..TQP.YPVQPPGNP.Y.P..LHL.Q.PP.TDAP.AYSEL...S....PG....P.....F...
Retrocopy MNSKGQCLTQPAYPVQPPGNPLY<PLTLHLSQVPPHTDAPSAYSELCHLSSA>APGGCHSPHHVSRFSLP

Parental  SLYLPMAQSVAVGPLGSTIPMAYYPVGPIYPPGSTVLVDGGYDAGARFGAGAAAGNIPPPPPGCPPNAAQ
          SLYLPMAQ.VA.GPLGSTIPMAYY....IYP.GS.VLV.GGYD.GARFGAGA.AG..PP..PGCPP.AAQ
Retrocopy SLYLPMAQ*VAIGPLGSTIPMAYY---LIYPSGSIVLVEGGYDIGARFGAGATAGSVPPLLPGCPPKAAQ

Parental  LAVMQGANVLVTQRKGNFFMGGSDGGYTIW
          LAVMQG..V.VTQ.KGNFFMGGS.G..TIW
Retrocopy LAVMQGTSVVVTQSKGNFFMGGSGGDHTIW

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	0.00 RPM
SRP021940_cerebellum	0.05 RPM	0.10 RPM
SRP021940_embryo	0.03 RPM	34.83 RPM
SRP021940_placental_villous	0.00 RPM	98.77 RPM
SRP021940_synovial_membrane	0.05 RPM	71.57 RPM
SRP021940_testis	0.00 RPM	67.84 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_286 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_286 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_286 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000298	1 retrocopy	retro_chof_85,
Dasypus novemcinctus	ENSDNOG00000009306	1 retrocopy	retro_dnov_1772,
Equus caballus	ENSECAG00000007313	1 retrocopy	retro_ecab_286 ,
Myotis lucifugus	ENSMLUG00000009959	1 retrocopy	retro_mluc_351,
Mus musculus	ENSMUSG00000000346	1 retrocopy	retro_mmus_1073,
Sorex araneus	ENSSARG00000003823	1 retrocopy	retro_sara_632,
Tupaia belangeri	ENSTBEG00000013232	1 retrocopy	retro_tbel_3228,
Vicugna pacos	ENSVPAG00000001156	2 retrocopies	retro_vpac_314, retro_vpac_568,