RetrogeneDB ID: retro_btau_439

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:47669365..47669866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX4
• Ensembl ID: ENSBTAG00000006165
• Aliases: None
• Description: Peroxiredoxin-4 [Source:UniProtKB/Swiss-Prot;Acc:Q9BGI2]

Sequence

>retro_btau_439
CTTGATGACTTTAAGGGGAAATATTTGGTGCTCTTCTATCCTTCAGATTTCACCTTTGTGTGTCCTATGGAAATTACTGC
TTTTGGTGACAAAGCCAATGAATTTCATAATGTAGAATCATTGCAGTGTCAGGTAGATTCCCACTTCAGCCACCTGACCC
AGATAAATACACTGAGGAAAAATGGTAGTTTGGGCCACATGAACATCATGCTCTTGTCAGATGTGACTAAATAAACTTCC
TGAGATTAGGGTGTGCTATTTGTTAGAAGGTCCTGTTCTTGCACTAAGAGGTCTCTTCATAATTGACCCCAGTGGAGTCA
TCAAACCTTTGAGTGTCAATGATCTCCCAGTGGGCCCAAGCGTGGGAGAGACCCTAGCTTGGTGAAGGCATTCCAGTTTG
TGCAATGCCATTGAGAAGTTTGCCTAGCCAGCTGGACACTGGATTCTCCTATAATCCAACTCCATCTGATTACTTCCAAG
AAATACTTTAAGAAGGTTAAT

Alignment

ORF - retro_btau_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.91 %
• Parental protein coverage: 61.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTDYRGKYLVFFFYPLDFTFVCPTEIIAFGDRIDEFRSINTEVVACSVDSQFTHLAWINTPRRQGGLGSI
          L.D..GKYLV.F.YP.DFTFVCP.EI.AFGD...EF...N.E...C.VDS.F.HL..INT.R..G.LG..
Retrocopy LDDFKGKYLVLF-YPSDFTFVCPMEITAFGDKANEFH--NVESLQCQVDSHFSHLTQINTLRKNGSLGHM

Parental  NIPLLADLNHQISKDYGV-YL-EDSGHTLRGLFIIDDKGILRQITLNDLPVGRSVDETL-RLVQAFQYTD
          NI.LL.D.....S.D.GV.YL.E.....LRGLFIID..G.......NDLPVG.SV.ETL..LV.AFQ...
Retrocopy NIMLLSDVTK*TS*D*GV>YLLEGPVLALRGLFIIDPSGVIKPLSVNDLPVGPSVGETL<SLVKAFQFVQ

Parental  KHGEVCPAGWKPGSETIIPDPAGKLKYFDKLN
          .H.EVC.A.W...S..I........KYF.K.N
Retrocopy CH*EVCLASWTLDSPIIQLHLITSKKYFKKVN

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	34.53 RPM
ERP005899_muscle	0.00 RPM	80.71 RPM
SRP017611_brain	0.00 RPM	13.52 RPM
SRP017611_kidney	0.00 RPM	30.29 RPM
SRP017611_liver	0.00 RPM	118.17 RPM
SRP030211_testis	0.00 RPM	76.07 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_439 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_439 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003642	2 retrocopies	retro_btau_1299, retro_btau_1446,
Bos taurus	ENSBTAG00000006165	1 retrocopy	retro_btau_439 ,
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562,
Cavia porcellus	ENSCPOG00000004185	1 retrocopy	retro_cpor_353,
Equus caballus	ENSECAG00000010085	1 retrocopy	retro_ecab_576,
Homo sapiens	ENSG00000123131	1 retrocopy	retro_hsap_3165,
Gorilla gorilla	ENSGGOG00000026790	1 retrocopy	retro_ggor_1351,
Myotis lucifugus	ENSMLUG00000004904	2 retrocopies	retro_mluc_2347, retro_mluc_2619,
Macaca mulatta	ENSMMUG00000021366	1 retrocopy	retro_mmul_2001,
Tupaia belangeri	ENSTBEG00000004454	5 retrocopies	retro_tbel_2164, retro_tbel_2467, retro_tbel_2522, retro_tbel_2811, retro_tbel_2978,
Tarsius syrichta	ENSTSYG00000000602	1 retrocopy	retro_tsyr_404,
Tursiops truncatus	ENSTTRG00000012368	1 retrocopy	retro_ttru_547,