RetrogeneDB ID: retro_btau_659

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:29909139..29910138(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX3
• Ensembl ID: ENSBTAG00000005027
• Aliases: GLRX3, PICOT, TXNL2
• Description: glutaredoxin-3 [Source:RefSeq peptide;Acc:NP_001030273]

Sequence

>retro_btau_659
ATGGCAGCAGGGGTGGCTGAGGTGGTGGCAGCTGTGGTAGAGGTTGGCTCAGCCCTGCAGTTTGAGGAGCTGCTGCGCCT
CAGAGCCAAGTCCTTTCTTGTGGTCCATTTCTGGGCACGATGAGCTCCTCAGTGTGCTCAGATGAACGACGTGATGGCAG
AGCTCGCCAAAGAGCACCCACAAGTTTCATTCGTGAAATTGGAAGCAGAAACTGTTCCTGAAGTATCTGAAAAATATGAA
ATTAGTTATGTTCCCACCTTCCTGTTTTTCAAGAATTCTCAGAAGATCTACTGATTAGATGGTGCCCATGGCCCCAGAGT
TGAGCAAAAAAGTTCAGCAACATGCGTCTGGTGGCTCCTTCTCACCCAGTGGTAGTGAGCACCTGAAGGAAGACCTCAAC
CAGCCCCTGAAGAAGTTATTTCTCGCTGCCCCCTGCATCCTGTTCATGAAAGGAACACCTCAGGAGCCACGCTGTGGTTT
CAGCAAGTAGATGGTGGAAATTCTTAACAAACATAATATTCAGTTTAGCAGTTTCCACATCTTCTCAGATGAAGTTCGCC
AGGCCCTCAAAACCTATTCCAATTGGCCCACGTATCCCCAGCTCTATGTTTCTGGAGAGCTCATAGGAGGACTTGATATA
ATTAAGGAGCTAGAAGCATCTAAAGAACTAGATATGATTTGCCCCAAAGCCCCCAAGTTAGAGGAAAGGCTCAAAGTAAG
GACAAATGAAGCTTCTCTGATGCTGTTTATGAAAGGAAACAAACAGGAAGCTGAGAGTGGCTTCAGCAGGCGATTCTGGA
AATATTAAATAGTACTGGGGTTGAATATGAGACATATGATATACTGGAGGATGAAGAAGTTCAGCAAGGATTAAAAGCTT
ACTCCAACTGGCTAACGTACCCTCAGCTGAATGTGAAGGGGGAGCTTGTCAGAGGACTGGACATCGTTAAGGAACGGAAA
GAAAATGGGGAGTTGCTGCCTATACTGAAAGGAGAAAAT

Alignment

ORF - retro_btau_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAGAAEAAAAVVEVGSAGQFEELLRLRAKSLLVVHFWAPWAPQCAQMNDVMAELAKEHQQVSFVKLEAE
          MAAG.AE..AAVVEVGSA.QFEELLRLRAKS.LVVHFWA..APQCAQMNDVMAELAKEH.QVSFVKLEAE
Retrocopy MAAGVAEVVAAVVEVGSALQFEELLRLRAKSFLVVHFWAR*APQCAQMNDVMAELAKEHPQVSFVKLEAE

Parental  AVPEVSEKYEISSVPTFLFFKNSQKIDRLDGAH-APELTKKVQRHASSGSFSPSGSEHPKEDLSLRLKKL
          .VPEVSEKYEIS.VPTFLFFKNSQKI..LDGAH.APEL.KKVQ.HAS.GSFSPSGSEH.KEDL...LKKL
Retrocopy TVPEVSEKYEISYVPTFLFFKNSQKIY*LDGAH>APELSKKVQQHASGGSFSPSGSEHLKEDLNQPLKKL

Parental  THAAPCMLFMKGTPQEPRCGFSKQMVEILNKHNIQFSSFDIFSDEEVRQGLKTYSSWPTYPQLYVSGELI
          ..AAPC.LFMKGTPQEPRCGFSK.MVEILNKHNIQFSSF.IFSD.EVRQ.LKTYS.WPTYPQLYVSGELI
Retrocopy FLAAPCILFMKGTPQEPRCGFSK*MVEILNKHNIQFSSFHIFSD-EVRQALKTYSNWPTYPQLYVSGELI

Parental  GGLDIIKELEASKELDTICPKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSRQ-ILEILNSTGIEYE
          GGLDIIKELEASKELD.ICPKAPKLEERLKV.TN.AS.MLFMKGNKQEA..GFSR..ILEILNSTG.EYE
Retrocopy GGLDIIKELEASKELDMICPKAPKLEERLKVRTNEASLMLFMKGNKQEAESGFSRR<ILEILNSTGVEYE

Parental  TFDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILKGEN
          T.DILEDEEV.QGLKAYSNW.TYPQL.VKGELV.GLDIVKE.KENGELLPILKGEN
Retrocopy TYDILEDEEVQQGLKAYSNWLTYPQLNVKGELVRGLDIVKERKENGELLPILKGEN

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	35.90 RPM
ERP005899_muscle	0.00 RPM	54.32 RPM
SRP017611_brain	0.00 RPM	35.58 RPM
SRP017611_kidney	0.00 RPM	50.20 RPM
SRP017611_liver	0.00 RPM	27.79 RPM
SRP030211_testis	0.30 RPM	141.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_659 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_659 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003257	1 retrocopy	retro_amel_1348,
Bos taurus	ENSBTAG00000005027	1 retrocopy	retro_btau_659 ,
Canis familiaris	ENSCAFG00000013280	1 retrocopy	retro_cfam_285,
Callithrix jacchus	ENSCJAG00000014400	1 retrocopy	retro_cjac_158,
Dasypus novemcinctus	ENSDNOG00000010387	1 retrocopy	retro_dnov_2110,
Gorilla gorilla	ENSGGOG00000010771	1 retrocopy	retro_ggor_2308,
Microcebus murinus	ENSMICG00000008544	2 retrocopies	retro_mmur_1394, retro_mmur_89,
Myotis lucifugus	ENSMLUG00000005483	1 retrocopy	retro_mluc_377,
Mus musculus	ENSMUSG00000031068	1 retrocopy	retro_mmus_2480,
Nomascus leucogenys	ENSNLEG00000027088	2 retrocopies	retro_nleu_2322, retro_nleu_249,
Ochotona princeps	ENSOPRG00000017309	1 retrocopy	retro_opri_462,
Pongo abelii	ENSPPYG00000002768	1 retrocopy	retro_pabe_2830,
Pan troglodytes	ENSPTRG00000003060	1 retrocopy	retro_ptro_2320,