RetrogeneDB ID: retro_btau_1709

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:74453851..74454341(-)
• Located in intron of: ENSBTAG00000017958

Retrocopy information

• Ensembl ID: ENSBTAG00000046495
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMAB
• Ensembl ID: ENSBTAG00000005178
• Aliases: MMAB, ATR
• Description: cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001073100]

Sequence

>retro_btau_1709
GGCCCGGGAGGTCGCCTTTGCTTGCGCGGGTGTCTTGGAGCCCGCGAGCTATTGTGTCCCCATTTCCAGAGTCGCAGCCC
CCAGGGTGTGGAAGATGGGGACAGGCCTCAGCCTTCCTCGAAGACTCCCTAGGTCCCCAAGATCTACACCAAAACAGGAG
ACAAAGGGTTTTCTAGCACCTTCACTGGAGAAAGACCACCCAAAGACGACCAGGTGTTTGAAGCTGTGGGAACTACAGAT
GAATTAAGTTCAGCCATTGGGTTTGCTATGGAATTAATTGCAGAAAAGGACCACCCGTTTGTGGAAGAGCTTCAGAGAAT
CCAGTGCTCCCTGTAGGACTTCAGCTCTGCCCTGGCGACTCCGCGCTCCTCAGCCAGAGAGGCTCATTTAAAACACGCCA
TGTTCGAGGCGGGGCTCATCCTGGAGCTGGAGCAGTGGATCGACAGATAACTCTCGCCAGCTGCCCCCACTCACCACTTT
CATCCTGCCT

Alignment

ORF - retro_btau_1709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.66 %
• Parental protein coverage: 67.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPGGRLGLRGCLGARKLLCPRFQSRGPQGVEDGDRPQPSSKTPKVPKIYTKTGDKGFSSTFTGERRSKDD
          GPGGRL.LRGCLGAR.LLCP.FQSR.PQGVEDGDRPQPSSKTP.VPKIYTKTGDKGFSSTFTGER..KDD
Retrocopy GPGGRLCLRGCLGARELLCPHFQSRSPQGVEDGDRPQPSSKTP*VPKIYTKTGDKGFSSTFTGERPPKDD

Parental  QVFEAVGTTDELSSAIGFVMELIAEKGHPFVEELQKLQSSRPDWSTIFATPLTVARQPPLSMGSSRAGPI
          QVFEAVGTTDELSSAIGF.MELIAEK.HPFVEELQ..Q.S..D.S...ATP...AR...L......AG.I
Retrocopy QVFEAVGTTDELSSAIGFAMELIAEKDHPFVEELQRIQCSL*DFSSALATPRSSAREAHLKHAMFEAGLI

Parental  LELEQWIDK-YSRQLPPLTAFILP
          LELEQWID...SRQLPPLT.FILP
Retrocopy LELEQWIDR>NSRQLPPLTTFILP

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	0.14 RPM	18.10 RPM
ERP005899_muscle	0.21 RPM	10.51 RPM
SRP017611_brain	0.27 RPM	3.79 RPM
SRP017611_kidney	0.30 RPM	5.51 RPM
SRP017611_liver	1.36 RPM	17.90 RPM
SRP030211_testis	0.09 RPM	7.78 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1709 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005178	1 retrocopy	retro_btau_1709 ,