RetrogeneDB ID: retro_btau_782

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:10634795..10635464(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000020774
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AK4
• Ensembl ID: ENSBTAG00000030674
• Aliases: AK4, AK 4, AK3L1
• Description: Adenylate kinase isoenzyme 4, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q0VCP1]

Sequence

>retro_btau_782
ATGGCTTCCAAACTCCTGCGTGCGGTCGTCCTTGGGCCGCCGGGCTCGGGCAAGGGCACCGTGTGCCAGAGGATAGCCCA
GAACTTTAGCCTTCAGCATCTCTCCAGCGGCCACTTCTTGCGGGAGAACATCAAGGCCAACACGGAAGTTGGTGATATGG
CAAAGCAATACATAGAGAAAGGCCTTTTGGTTCCCGATCATGGGATCACACGCCTCATGCTGTTGGAGTTGGAGAACAGG
CGCGGCGAGCACTGGCTACTTGATGGTTTTCCTCGAACATTAGTTCAGGCTGAAGCCTTGGACAGACTATGTGACCTGGA
TCTAGTGATCACTTTGAACATTGCATTTGAAACGCTCAAAGATCGTCTCAGCCGACGTTGGATTCACCCTCCCAGTGGAA
GGGTATATAACCTGGACTTCAACCCACCTCATGTACATGGCATGGATGACGTCACTGGTGAGCCACTTGTCCAGCAGGAG
GATGACAAACCGGAAGCAGTTGCTGCCAGGCTAAGGCAGTACAAGGATGTGGCAAGACCCGTCATCGAGCTGTACAAGAG
CCGAGGAGTGCTCCACCAGTTTTCAGGAACCGAGACTAACAAAATCTGGCCCTATGTTTACACGCTTTTCTCGAACAAGA
TCACACCTGTTCAGTCCAAAGAAGCCTAC

Alignment

ORF - retro_btau_782 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASKLLRAVILGPPGSGKGTVCQRIAQNFGLQHLSSGHFLRENIKANTEVGDMAKQYIEKGLLVPDHVIT
          MASKLLRAV.LGPPGSGKGTVCQRIAQNF.LQHLSSGHFLRENIKANTEVGDMAKQYIEKGLLVPDH.IT
Retrocopy MASKLLRAVVLGPPGSGKGTVCQRIAQNFSLQHLSSGHFLRENIKANTEVGDMAKQYIEKGLLVPDHGIT

Parental  RLMLLELENRRGEHWLLDGFPRTLVQAEALDRLCDLDLVITLNIPFETLKDRLSRRWIHPPSGRVYNLDF
          RLMLLELENRRGEHWLLDGFPRTLVQAEALDRLCDLDLVITLNI.FETLKDRLSRRWIHPPSGRVYNLDF
Retrocopy RLMLLELENRRGEHWLLDGFPRTLVQAEALDRLCDLDLVITLNIAFETLKDRLSRRWIHPPSGRVYNLDF

Parental  NPPHVHGMDDVTGEPLVQQEDDKPEAVAARLRQYKDVAKPVIELYKSRGVLHQFSGTETNKIWPYVYTLF
          NPPHVHGMDDVTGEPLVQQEDDKPEAVAARLRQYKDVA.PVIELYKSRGVLHQFSGTETNKIWPYVYTLF
Retrocopy NPPHVHGMDDVTGEPLVQQEDDKPEAVAARLRQYKDVARPVIELYKSRGVLHQFSGTETNKIWPYVYTLF

Parental  SNKITPVQSKEAY
          SNKITPVQSKEAY
Retrocopy SNKITPVQSKEAY

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	16.73 RPM
ERP005899_muscle	0.00 RPM	1.53 RPM
SRP017611_brain	0.32 RPM	16.54 RPM
SRP017611_kidney	0.41 RPM	150.25 RPM
SRP017611_liver	0.15 RPM	5.36 RPM
SRP030211_testis	0.07 RPM	1.28 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_782 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_782 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014969	1 retrocopy	retro_amel_728,
Bos taurus	ENSBTAG00000017147	1 retrocopy	retro_btau_323,
Bos taurus	ENSBTAG00000030674	1 retrocopy	retro_btau_782 ,
Macaca mulatta	ENSMMUG00000001079	3 retrocopies	retro_mmul_104, retro_mmul_1680, retro_mmul_2080,