RetrogeneDB ID: retro_btau_253

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:41647960..41648566(+)
• Located in intron of: ENSBTAG00000010091

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.56566
• Ensembl ID: ENSBTAG00000035556
• Aliases: None
• Description: protein CDV3 homolog [Source:RefSeq peptide;Acc:NP_001178969]

Sequence

>retro_btau_253
GTGGCTGAGACGGAGGAGCGGAGCCTAGACAACTTCTTCACCAAGAGAGATAAAAAGAAGAAGGAGCGGAGCAACCAGGC
GGCGAGCGCGGCGGGAGGCGCTGGCGGGAGCAGTGGAGCCACGGACTCAGCGGGCGGTGGGGCAGGCGTGGGGACCCGGC
CAGGCGATAGCGGGACCGCAGGCCTGGGGGCCACTGGCCCTGGGGCCGCCACCAAGGTTGTGACAAAGGAGGAAGATGAG
TAGAAAGAATTTGAGCAAAAAGAAGTTGATTACAGCGGCCTAAGAGTTCAAGCAATGCAAATAAGTGAAAAGGAAGAAGA
TGAAAAGAGAGAAGATCCAAGTGATAATTGGGAAGAAGGTGGAGGTGGTGGTGGTGATGGTGTAGAAAAATCTTCAGGCC
CTTGGAATAAAACTGCTCTAGTACAAGTACCTCCTGCTCCAGTAGTTGTTACAGAAACCCCAGAACCAACAATGACTAGT
GGCGTGTATAGGCCTCCTGGAGCCAGGTTGACCACAACAAGGAAAGCACCACAAGGACCACCAGAAATCTATAGTGACAC
GCACCCATCCCTGCAGTCCACTACCAAGCATGTAGAAAGCTGGAAA

Alignment

ORF - retro_btau_253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.05 %
• Parental protein coverage: 81.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAETEERSLDNFFAKRDKKKKKERSNRAASAASAAGGAGGSSGATGAAGGGAGARTRPGDSGTAGVGATG
          .AETEERSLDNFF.KRDKKKK.ERSN....AASAAGGAGGSSGAT..AGGGAG..TRPGDSGTAG.GATG
Retrocopy VAETEERSLDNFFTKRDKKKK-ERSNQ---AASAAGGAGGSSGATDSAGGGAGVGTRPGDSGTAGLGATG

Parental  PGAATKVVTKEEDEWKEFEQKEVDYSGLRVQAMQISSEKEEDEVEKREDPSDNWEEGGGGGG-GVEKSSG
          PGAATKVVTKEEDE.KEFEQKEVDYSGLRVQAMQIS.EKEED..EKREDPSDNWEEGGGGGG.GVEKSSG
Retrocopy PGAATKVVTKEEDE*KEFEQKEVDYSGLRVQAMQIS-EKEED--EKREDPSDNWEEGGGGGGDGVEKSSG

Parental  PWNKTAPVQAPPAPVVVTETPEPTMTSGVYRPPGARLTTTRKAPQGPPEIYSDTQFPSLQSTAKHVESRK
          PWNKTA.VQ.PPAPVVVTETPEPTMTSGVYRPPGARLTTTRKAPQGPPEIYSDT..PSLQST.KHVES.K
Retrocopy PWNKTALVQVPPAPVVVTETPEPTMTSGVYRPPGARLTTTRKAPQGPPEIYSDTH-PSLQSTTKHVESWK

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	133.88 RPM
ERP005899_muscle	0.21 RPM	87.74 RPM
SRP017611_brain	0.46 RPM	81.17 RPM
SRP017611_kidney	0.95 RPM	170.29 RPM
SRP017611_liver	0.68 RPM	104.20 RPM
SRP030211_testis	0.28 RPM	218.37 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_253 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_253 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253 ,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Callithrix jacchus	ENSCJAG00000002998	1 retrocopy	retro_cjac_2928,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus	ENSECAG00000015689	2 retrocopies	retro_ecab_444, retro_ecab_636,
Homo sapiens	ENSG00000091527	1 retrocopy	retro_hsap_2678,
Gorilla gorilla	ENSGGOG00000027821	1 retrocopy	retro_ggor_1869,
Myotis lucifugus	ENSMLUG00000009864	1 retrocopy	retro_mluc_1296,
Mus musculus	ENSMUSG00000032803	10 retrocopies	retro_mmus_1266, retro_mmus_2405, retro_mmus_2408, retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Nomascus leucogenys	ENSNLEG00000003470	1 retrocopy	retro_nleu_1181,
Oryctolagus cuniculus	ENSOCUG00000012748	1 retrocopy	retro_ocun_1106,
Ochotona princeps	ENSOPRG00000003600	3 retrocopies	retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii	ENSPPYG00000025898	1 retrocopy	retro_pabe_2301,
Pan troglodytes	ENSPTRG00000015409	1 retrocopy	retro_ptro_1805,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,
Tarsius syrichta	ENSTSYG00000011401	2 retrocopies	retro_tsyr_1381, retro_tsyr_1759,