RetrogeneDB ID: retro_btau_1003

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:11198524..11198805(+)
• Located in intron of: ENSBTAG00000014253

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLO1
• Ensembl ID: ENSBTAG00000012703
• Aliases: None
• Description: lactoylglutathione lyase [Source:RefSeq peptide;Acc:NP_001076965]

Sequence

>retro_btau_1003
TCATGGGCCATCTCCAGAAAAGCTGCCCTTGAACTGACACACAATTGGAGCGCTGAAGACACTGGGACCAGAGTTACCAC
AGTGGTGATTCAGGCCCTCAGGGATTTGGTCACATTGAAATTGCTATTCCTGATGTTCACGGGGCTTGTAAAATGTTTGA
AAAACTGGGAGTCCAGTGTGTAGAGAAACCTGATGATGGTAAAATGAAAGGCCTGGCATTTATTCACAATCCTGATGGCT
TCTGGAATGAAATTTTGAATCCTAACAAAATGATGACTGTT

Alignment

ORF - retro_btau_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.58 %
• Parental protein coverage: 51.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AWVFSRKATLELTHNWGTEDDET-QSYHSGNSDPRGFGHIGIAVPDVHGACKRFEELGIKFVKKPDDGKM
          .W..SRKA.LELTHNW..ED..T.QSYHSG.S.P.GFGHI.IA.PDVHGACK.FE.LG...V.KPDDGKM
Retrocopy SWAISRKAALELTHNWSAEDTGT<QSYHSGDSGPQGFGHIEIAIPDVHGACKMFEKLGVQCVEKPDDGKM

Parental  KGLAFIQDPDGYWIEILNPNTMITI
          KGLAFI..PDG.W.EILNPN.M.T.
Retrocopy KGLAFIHNPDGFWNEILNPNKMMTV

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	352.40 RPM
ERP005899_muscle	0.05 RPM	71.53 RPM
SRP017611_brain	0.00 RPM	70.71 RPM
SRP017611_kidney	0.00 RPM	104.67 RPM
SRP017611_liver	0.00 RPM	125.42 RPM
SRP030211_testis	0.02 RPM	11.78 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1003 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1003 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012703	2 retrocopies	retro_btau_1003 , retro_btau_1513,
Cavia porcellus	ENSCPOG00000010050	1 retrocopy	retro_cpor_1482,
Dasypus novemcinctus	ENSDNOG00000019598	6 retrocopies	retro_dnov_1016, retro_dnov_1064, retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
Dipodomys ordii	ENSDORG00000006369	1 retrocopy	retro_dord_21,
Macropus eugenii	ENSMEUG00000005978	1 retrocopy	retro_meug_1641,
Mus musculus	ENSMUSG00000024026	1 retrocopy	retro_mmus_1902,
Otolemur garnettii	ENSOGAG00000007945	2 retrocopies	retro_ogar_2541, retro_ogar_681,
Rattus norvegicus	ENSRNOG00000000541	2 retrocopies	retro_rnor_1012, retro_rnor_1024,
Sus scrofa	ENSSSCG00000027778	1 retrocopy	retro_sscr_853,
Ictidomys tridecemlineatus	ENSSTOG00000005821	1 retrocopy	retro_itri_1626,
Tupaia belangeri	ENSTBEG00000014386	1 retrocopy	retro_tbel_4376,
Tursiops truncatus	ENSTTRG00000004664	1 retrocopy	retro_ttru_90,