RetrogeneDB ID: retro_btau_663

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:41290986..41291473(+)
• Located in intron of: ENSBTAG00000016679

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.88393
• Ensembl ID: ENSBTAG00000034598
• Aliases: BOD1, FAM44B
• Description: biorientation of chromosomes in cell division protein 1 [Source:RefSeq peptide;Acc:NP_001069668]

Sequence

>retro_btau_663
GGGGACACCCATGTGATGGGCAGTGGCAGTGCAGGCCAGGCCTCCACGGGAGCCACGATGGGCGCTGTCGGGAGCGGTGG
CCCCATCAGCCCGGCCTCAGTGCCTCTGCGGGACCTCGCACTCATCACGCTCATCTTGGAGCAGTTCAAGAACCAGGACC
TGTTTGACAGCTTCTGCCAGGACTGCCTGGCCCAGATGGACATCAAGCCAGCTTACCAAAACCAGAGGCAGAAAGTGGAT
AATTTTGTTGTCAACACATCTGGATAAGCAGGAATGGAATCCTTCTATGAACAAAAACCAGCTGTAAAATGGTCTGAGGC
AGAGTGTGGTTCAGTCAGGGATGTTGGAAGCTGGAGTGGACAGAATTCTTTCTGAGGTGGTGGATCCCAAACTAACCCAT
ATCTTCTGGCCACAAACAGAATGAGCAATTCATGAATTCCTGGCGGCCCAGAAAAAAGAAGTTGTTCCAGCGCTGCCCGC
CGCCCCC

Alignment

ORF - retro_btau_663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.89 %
• Parental protein coverage: 89.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSTGAVGGGGAGPASAGAAAGGGGAGGSGGPINPASLPPGDPQLIALIVEQLKSRGLFDSFRRDCLADVD
          G.T...G.G.AG.AS.GA.....GA.GSGGPI.PAS.P..D..LI.LI.EQ.K...LFDSF..DCLA..D
Retrocopy GDTHVMGSGSAGQASTGATM---GAVGSGGPISPASVPLRDLALITLILEQFKNQDLFDSFCQDCLAQMD

Parental  TKPAYQNLRQKVDNFV-STHLDKQEWNPTMNKNQLRNGLRQSVVQSGMLEAGVDRIISQVVDPKLNHIFR
          .KPAYQN.RQKVDNFV.STHLDKQEWNP.MNKNQL.NGLRQSVVQSGMLEAGVDRI.S.VVDPKL.HIF.
Retrocopy IKPAYQNQRQKVDNFV>STHLDKQEWNPSMNKNQL*NGLRQSVVQSGMLEAGVDRILSEVVDPKLTHIFW

Parental  PQIERAIHEFLAAQKKEAVPAPPPEP
          PQ.E.AIHEFLAAQKKE.VPA.P..P
Retrocopy PQTE*AIHEFLAAQKKEVVPALPAAP

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	8.29 RPM
ERP005899_muscle	0.11 RPM	6.76 RPM
SRP017611_brain	0.00 RPM	15.35 RPM
SRP017611_kidney	0.00 RPM	9.36 RPM
SRP017611_liver	0.00 RPM	4.76 RPM
SRP030211_testis	0.04 RPM	30.47 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_663 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_663 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034598	1 retrocopy	retro_btau_663 ,
Canis familiaris	ENSCAFG00000016776	1 retrocopy	retro_cfam_1374,
Callithrix jacchus	ENSCJAG00000031971	4 retrocopies	retro_cjac_1154, retro_cjac_1515, retro_cjac_1536, retro_cjac_953,
Homo sapiens	ENSG00000145919	3 retrocopies	retro_hsap_102, retro_hsap_1867, retro_hsap_993,
Gorilla gorilla	ENSGGOG00000010925	2 retrocopies	retro_ggor_1365, retro_ggor_794,
Microcebus murinus	ENSMICG00000002626	1 retrocopy	retro_mmur_1126,
Macaca mulatta	ENSMMUG00000013793	2 retrocopies	retro_mmul_803, retro_mmul_869,
Mus musculus	ENSMUSG00000044502	1 retrocopy	retro_mmus_3661,
Nomascus leucogenys	ENSNLEG00000000476	1 retrocopy	retro_nleu_1224,
Oryctolagus cuniculus	ENSOCUG00000014283	1 retrocopy	retro_ocun_1071,
Otolemur garnettii	ENSOGAG00000001107	3 retrocopies	retro_ogar_1477, retro_ogar_2663, retro_ogar_3112,
Pongo abelii	ENSPPYG00000016057	2 retrocopies	retro_pabe_1567, retro_pabe_1587,
Pan troglodytes	ENSPTRG00000017544	2 retrocopies	retro_ptro_1282, retro_ptro_757,
Ictidomys tridecemlineatus	ENSSTOG00000013505	1 retrocopy	retro_itri_1164,
Tupaia belangeri	ENSTBEG00000014046	1 retrocopy	retro_tbel_3451,
Tarsius syrichta	ENSTSYG00000007617	1 retrocopy	retro_tsyr_818,
Tursiops truncatus	ENSTTRG00000000384	2 retrocopies	retro_ttru_1004, retro_ttru_457,
Vicugna pacos	ENSVPAG00000004260	1 retrocopy	retro_vpac_452,