RetrogeneDB ID: retro_ecab_130

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:59208650..59209096(+)
• Located in intron of: None

Retrocopy information

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

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_130
AAGGTCTTCGTGGGAGGCCGTGGCTTCAGCACCGATGGGCAGGCGCTAGATGACCGCTTCAGCAGCTTCGGGCCTATTTC
TGAGGTGGTTGTTCTCAAAGACCAGGAGACTCAGCAATCCTGGGGTTTTGGCTTCATCACCTTCACCCATCCACAGCGTG
CCTCAGATGCCACGAGAGCCCTGAATGGAGAGTCCTGGATGGTTGCCAGATCCCTGTGGACCACGCAGGCAAGTCAGCCC
AGGGAACCAGAGGGGGTGCCCTTGGGGCCCATGGGCGTGGTCACGGCCAGTCTAGAGGCGGTGGGGACCTGGGCTATGGG
AGTGGCAGGTATGACAGTGGACCTGAAGGATATAGATACAGATATAGAAGGTCCAGAGACTAAGGTGGCAGAAGCCAGGG
TGGTTATGACTGCGACACAGGAGGAAATAACAGAGCCAACTACAAC

Alignment

ORF - retro_ecab_130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.33 %
• Parental protein coverage: 95.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMRAMNGES-LDGR
          K.FVGG..F.TD.QAL.D.FSSFGPISEVVV.KD.ETQ.S.GFGFITFT.P..ASDA.RA.NGES.LDG.
Retrocopy KVFVGGRGFSTDGQALDDRFSSFGPISEVVVLKDQETQQSWGFGFITFTHPQRASDATRALNGES<LDGC

Parental  QIRVDHAGKSARGTRGGAFGAHGRGRGYSRGGGDQGYGSGRYDSRPGGYGYGYGRSRDYGGRNQGGYDRY
          QI.VDHAGKSA.GTRGGA.GAHGRG.G.SRGGGD.GYGSGRYDS.P.GY.Y.Y.RSRD.GGR.QGGYD..
Retrocopy QIPVDHAGKSAQGTRGGALGAHGRGHGQSRGGGDLGYGSGRYDSGPEGYRYRYRRSRD*GGRSQGGYDCD

Parental  SGGNYRDNYD
          .GGN.R.NY.
Retrocopy TGGNNRANYN

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	231.34 RPM
SRP021940_cerebellum	0.16 RPM	114.10 RPM
SRP021940_embryo	0.03 RPM	183.38 RPM
SRP021940_placental_villous	0.05 RPM	106.66 RPM
SRP021940_synovial_membrane	0.16 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_130 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_130 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,