RetrogeneDB ID: retro_btau_1144

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:35280886..35281344(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSBTAG00000025848
• Aliases: None
• Description: None

Sequence

>retro_btau_1144
GAAGAAGGGAAGCTCTTTGTGGGAGGACTCAACTTCAGCCCTGATGGGCGCACTCTGGAAGATCATTTCAGCATCTTCTG
ACCTGTTTCTGGGGTGGTCAAGGTCAAAGACTGGAAGACACAGCTATCCCAGGGTTTTGGTTTCACCACCTTCAACAGTC
CAGAGTGTGCCTCTGATGCTATGAGAGCCTTGAATGGAAAGTCTCTGATAATTGTCAGATCCATGTAGACCACTCGGGCA
AGTTGGCCTCGGGGAACAAGAGGAGGTGACTTTGAGCCTGTGGGTGTGGTCACAGTTACTCTAGAGGAGGTGGGGACCGG
GACTATGGAAGTGACAAGTATGACAGTTGACCTGGAGGATATGGATATGGACATGGAAGATCCACAGACTATGGTGGCAG
AAGTCAGGGTGGTTATGACCACTATTTAGGAGGAAATTACAGGGACAATTATGACAAC

Alignment

ORF - retro_btau_1144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.19 %
• Parental protein coverage: 98.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEGKLFVGGLNFNTDERALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASNAMRAMNGESL-
          EEGKLFVGGLNF..D.R.LEDHFS.F.P.S.VV.VKD..TQ.S.GFGF.TF..PE.AS.AMRA.NG.SL.
Retrocopy EEGKLFVGGLNFSPDGRTLEDHFSIF*PVSGVVKVKDWKTQLSQGFGFTTFNSPECASDAMRALNGKSL<

Parental  DGRQIRVDHAGKSARGSRGGAFGGYERGRGYPRGGGDQGYGSGRYDNRPGAYGFGYGYGYGRSRDYGGRS
          D..QI.VDH.GK.A.G...........G..Y.RGGGD..YGS..YD..PG....GYGYG.GRS.DYGGRS
Retrocopy DNCQIHVDHSGKLASGNKRR*L*ACGCGHSYSRGGGDRDYGSDKYDS*PG----GYGYGHGRSTDYGGRS

Parental  QGGYDRYSGGNYRDNYDN
          QGGYD.Y.GGNYRDNYDN
Retrocopy QGGYDHYLGGNYRDNYDN

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
ERP005899_liver	0.00 RPM	13.99 RPM
ERP005899_muscle	0.00 RPM	16.79 RPM
SRP017611_brain	0.00 RPM	14.66 RPM
SRP017611_kidney	0.00 RPM	16.95 RPM
SRP017611_liver	0.00 RPM	8.38 RPM
SRP030211_testis	0.00 RPM	64.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1144 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 50 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	ENSBTAG00000001697	2 retrocopies	retro_btau_1245, retro_btau_850,
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144 ,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
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,