RetrogeneDB ID: retro_btau_543

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:43511757..43512108(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX2
• Ensembl ID: ENSBTAG00000015972
• Aliases: None
• Description: Glutaredoxin-2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q32L67]

Sequence

>retro_btau_543
GTTTCTGCCTCTGCTAAGGGGAATAGCACATCATCATCTTTGCGGAACTCAGCAACTGCTCCTGTGAATCAGATCCAAGA
AGCAATTTCTGATAATTATGTAATAATTTTCTCAAAAACATTTTGTTCTTACAGTACAATGGTAAACATGCTTTTGCATG
ACATGAATGTTAATTATAAAGTTGTGGGATTCGACATGCTTGAATATAGAAGCCAGATTCAAGATGTTTTTTACAAAGTG
ACCAGTGAAAGAAGTGTGCTAAAAATATTTGTCAATGGAACTTTTATTGAAAGTACAATAGATACTTATAGGCTTCACAG
AGAAGAGAAATTGCTTCTACTATTTCATCAG

Alignment

ORF - retro_btau_543 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.38 %
• Parental protein coverage: 74.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISGSGMGNSTSSSLGNAATAPVNQIQETISNNCVVIFSKTSCSYCTMAKNLFHDMNVNYKVVELDMLEYG
          .S.S..GNSTSSSL.N.ATAPVNQIQE.IS.N.V.IFSKT.CSY.TM...L.HDMNVNYKVV..DMLEY.
Retrocopy VSASAKGNSTSSSLRNSATAPVNQIQEAISDNYVIIFSKTFCSYSTMVNMLLHDMNVNYKVVGFDMLEYR

Parental  SQFQDALHKMTGERTVPRIFVNGTFIGGATDTHRLHKEGKLLPLVHQ
          SQ.QD...K.T.ER.V..IFVNGTFI....DT.RLH.E.KLL.L.HQ
Retrocopy SQIQDVFYKVTSERSVLKIFVNGTFIESTIDTYRLHREEKLLLLFHQ

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	9.52 RPM
ERP005899_muscle	0.00 RPM	10.87 RPM
SRP017611_brain	0.00 RPM	4.98 RPM
SRP017611_kidney	0.00 RPM	9.72 RPM
SRP017611_liver	0.00 RPM	7.70 RPM
SRP030211_testis	0.00 RPM	39.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_543 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_543 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_543 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015972	1 retrocopy	retro_btau_543 ,
Choloepus hoffmanni	ENSCHOG00000007274	1 retrocopy	retro_chof_2375,
Callithrix jacchus	ENSCJAG00000008562	1 retrocopy	retro_cjac_643,
Equus caballus	ENSECAG00000015376	1 retrocopy	retro_ecab_169,
Felis catus	ENSFCAG00000025580	1 retrocopy	retro_fcat_733,
Myotis lucifugus	ENSMLUG00000015734	1 retrocopy	retro_mluc_1008,
Tupaia belangeri	ENSTBEG00000011216	1 retrocopy	retro_tbel_1638,
Drosophila melanogaster	FBgn0036820	1 retrocopy	retro_dmel_4,