RetrogeneDB ID: retro_btau_380

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:75023370..75023717(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A3
• Ensembl ID: ENSBTAG00000046467
• Aliases: None
• Description: Protein tyrosine phosphatase type IVA 3 [Source:UniProtKB/Swiss-Prot;Acc:A2VDT1]

Sequence

>retro_btau_380
GCCCTTGTGGATAAAGAAGGCATTCATGTTCACAAGTGGCCTTTTGATGATGGTGTCCCACCATCTAGCCAGATTGCTGA
TGACTGGTTAAATCTTTAAAAAAATTAAGCTTTGTGAAAACATGGAAACATGGTTTTGTGTTGCTACCAATGTGCAGGTC
TTAGCAGAGTCCAGTGCTTGTCATCCTGATATTAACTGAAAGTAGAATGAAATATGAGGATTCAGTGCAGTTCATAAAAC
AAAAGAGGGGGTGGGGATTTTAATAACAAGGAACTTTTGTACATGAAGTATTGTTCTAAAATATGAATGTGCTTCAAAAC
TCCAATGGCCATAGAAGCAACTGTTGT

Alignment

ORF - retro_btau_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.22 %
• Parental protein coverage: 67.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  APLEKDGITVVDWPFDDGAPPPGKVVEDWLSLLKN-KFCDDPGS--CVAVH-CVAGLGR-APVLVALALI
          A...K.GI.V..WPFDDG.PP......DWL.L.KN.K.C.......CVA...C.AGL.R..PVLV.L.L.
Retrocopy ALVDKEGIHVHKWPFDDGVPPSSQIADDWLNL*KN>KLCENMETWFCVATN<C-AGLSR<SPVLVILILT

Parental  ESGMKYEDAIQFIRQKR-RGAINSKQLTYLEKYRPKQRLRFKDPHA-HKTKCC
          ES.MKYED..QFI.QKR..G..N.K.L.Y..KY..K....FK.P.A.H...CC
Retrocopy ESRMKYEDSVQFIKQKR>GGDFNNKELLYM-KYCSKI*MCFKTPMA<HRSNCC

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	1.59 RPM
ERP005899_muscle	0.00 RPM	0.84 RPM
SRP017611_brain	0.00 RPM	3.20 RPM
SRP017611_kidney	0.00 RPM	1.60 RPM
SRP017611_liver	0.00 RPM	3.47 RPM
SRP030211_testis	0.00 RPM	4.37 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_380 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002275	3 retrocopies	retro_btau_1051, retro_btau_1186, retro_btau_859,
Bos taurus	ENSBTAG00000039121	1 retrocopy	retro_btau_638,
Bos taurus	ENSBTAG00000046467	1 retrocopy	retro_btau_380 ,
Gorilla gorilla	ENSGGOG00000010609	1 retrocopy	retro_ggor_843,
Microcebus murinus	ENSMICG00000006858	4 retrocopies	retro_mmur_269, retro_mmur_349, retro_mmur_642, retro_mmur_889,
Macaca mulatta	ENSMMUG00000019392	1 retrocopy	retro_mmul_1132,