RetrogeneDB ID: retro_ecab_589

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 22:34489900..34490368(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002141
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSECAG00000024257
• Aliases: None
• Description: RNA binding motif (RNP1, RRM) protein 3 [Source:HGNC Symbol;Acc:9900]

Sequence

>retro_ecab_589
ATGTCCTCTGAAGAGGGGAAGCTCTTGGCGGGACGGTTCAACTTCCACATCGATGAGTGGCCTCTGGGAGACCTCTTCAG
CAGCTCCGGGCCTCTTTCTGAGGTGGTCATTGCCGAGGACCAGGCGACTCAGCAGTCCCAGCGTTTCGGCTTCATCACCT
TCACCAATCCAGAGTGGGCCTCAGACGCCATGAGAGCCCTGAACGGAGAGTCTCTGGATGGTTGCCAGATCCGTGGGGAC
CACGCAGGCAAGTTGGCTCCAGGGGACCGGAAGGGATGCCTAGGGGCTCATGGGTGTCGTCGCAGCTACTCTAGAGGTGG
TGGGGACCAGGGCTATGGGAGTGGCAGGTATGACAGTTGACCTGGAGGATATGGATACGGATATGGAAGGTCAGGAGACT
ATGGTGGCAGAAGTCAGGGTGGTTATGACTGCTACTCAGGAGGAAATCACAGAGACCGTTACGACAAC

Alignment

ORF - retro_ecab_589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMRAMNGE
          MSSEEGKL..G..NF..DE..L.D.FSS.GP.SEVV...D..TQ.S..FGFITFTNPE.ASDAMRA.NGE
Retrocopy MSSEEGKLLAGRFNFHIDEWPLGDLFSSSGPLSEVVIAEDQATQQSQRFGFITFTNPEWASDAMRALNGE

Parental  SLDGRQIRVDHAGKSARGTRGGAFGAHGRGRGYSRGGGDQGYGSGRYDSRPGGYGYGYGRSRDYGGRNQG
          SLDG.QIR.DHAGK.A.G.R.G..GAHG..R.YSRGGGDQGYGSGRYDS.PGGYGYGYGRS.DYGGR.QG
Retrocopy SLDGCQIRGDHAGKLAPGDRKGCLGAHGCRRSYSRGGGDQGYGSGRYDS*PGGYGYGYGRSGDYGGRSQG

Parental  GYDRYSGGNYRDNYDN
          GYD.YSGGN.RD.YDN
Retrocopy GYDCYSGGNHRDRYDN

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	0.12 RPM	231.34 RPM
SRP021940_cerebellum	0.00 RPM	114.10 RPM
SRP021940_embryo	0.28 RPM	183.38 RPM
SRP021940_placental_villous	0.38 RPM	106.66 RPM
SRP021940_synovial_membrane	0.08 RPM	165.01 RPM
SRP021940_testis	0.00 RPM	40.60 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_589 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_589 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_589 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589 ,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,