RetrogeneDB ID: retro_btau_300

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:71846274..71846568(-)
• Located in intron of: ENSBTAG00000048195

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.24043
• Ensembl ID: ENSBTAG00000046385
• Aliases: None
• Description: ras-related protein Rab-5A [Source:RefSeq peptide;Acc:NP_001069654]

Sequence

>retro_btau_300
AATGAGGGGTCCTTTGTAAGAACAAAAAACTAGGTTAAATTACTTCAGAGAGAAGTGAGTCCTAACACTGTCATAACTTT
ACCAGGAAAGTAGGTCGATCTAGAAAAAATGGGCTGAGATTTCCAGGAAGCACAGTCCTGTGCAAATGACAAGGTATTCA
CGAAGACATCATCTCAAACAACAATGAATGTAAATAAAATATTCACAGTAATAGCTAAAAAGTTGCCAAGGAATGAACTA
CAGAATCCAGGACCAAATTCTGCCAGAGCAAGAGCAGCAGACCTTACTGAACCC

Alignment

ORF - retro_btau_300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.39 %
• Parental protein coverage: 62.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEI
          NE.SF.R.KN.VK.LQR..SPN.VI.L.G...DL..K...DFQEAQS.A.D....F..TS..T.MNVN.I
Retrocopy NEGSFVRTKN*VKLLQREVSPNTVITLPGK*VDL-EKMG*DFQEAQSCANDK--VFTKTSSQTTMNVNKI

Parental  FMAIAKKLPKNEPQNPGANSTRGRGVDLTEP
          F..IAKKLP.NE.QNPG.NS.R.R..DLTEP
Retrocopy FTVIAKKLPRNELQNPGPNSARARAADLTEP

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	23.29 RPM
ERP005899_muscle	0.00 RPM	18.79 RPM
SRP017611_brain	0.00 RPM	51.43 RPM
SRP017611_kidney	0.00 RPM	29.87 RPM
SRP017611_liver	0.00 RPM	20.92 RPM
SRP030211_testis	0.00 RPM	33.96 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_300 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_300 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300 ,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,