RetrogeneDB ID: retro_rnor_2322

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:114989415..114990627(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Bckdk
• Ensembl ID: ENSRNOG00000019485
• Aliases: None
• Description: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q00972]

Sequence

>retro_rnor_2322
ATGATACTGACTTCAGTGCTGGGCAGCGGCCCTCGGAGCGGGTCTTAACTTTGGCCCCCTCTTAGGGTCCTCACTGTCAT
TCCGGGTTCGCTCAACATCAGCCACCGATACACACCATGTAGAGCTGGCCAGGGAACGCTCCAAGACTGTTACCTCCTTT
TACAACCAGTCAGCTATTGATGTGGTAGCAGAGAAGCCCTCAGTCTGCCTCACTCCCACCATGATGCTCTATTCTGGTCA
CTCACAGGATGGCAGCCACCTTCTGAAAAGTGGCTGCTACTTGCAGCAAGAGTTATCGGTGAGGATCGCTCACCGCATCA
AGGCCTTCCGTAGTCTTCCTTTCATCATTGGTTGCAACCCTACCATATTGCGTGTGCACGAGCTTTACGTCCGGGTCTTC
CAGAAGCTGACAGACTTCCCTCCGATCAAGGACCAGGCAGACTAGGCCCAGTATTGCCAGCTGGTGCGACAGCTGCTAGA
TGACCACAAGGATGTGGTGACCCTGTTAGCTGAGGGTCTTCGTGAGAGCCGGAAACACATAGAGGATGAAAAGCTAGTCT
GGTACTTGCTGGATAAAACACTAAAGTCCAGACTTGGGATCCGAATGCTGGCTACTCACCACTTGGCGCTACATGAAGAC
AAGCCTGATTTTGTTGGCATCATCTGCACTCGTCTGTCACCCAAGAAGATTATTGAGAAGTGGGTGGATTTTGCCAGATG
CCTGTGTGAGCACAAGTATGGCAATGCCCCTCGAGTCCGCATCAATGGGCATGTGGCTGCCGGTTTCCCCTTCATTCCTA
TGCGGCTGGACTATATCCTGCCTGAGCTCCTCAAGAACGCCGTGAGAGCCACAATGGGGAGTCACCTAGACACGCCCTAC
AATGTTCCTGATGTGGTCATCACCATCGCCAGTAATGTTGTGGATCTCATCATCAGGATCTCAGACCAGGGTGGAGGAAT
CGCTCATAATGACCTGGATCGAGTCATGGACCACCACTTCACCACATCTGAGGCCAGCACCCAGGACCCCCAAATCGGCC
CCCTCTTCGGCCACCTGGATATGCACAGTGGACCTATGCATGGCTTTGGCTTCCGGTTGCCTATGCGGAGTATCTCGTTG
GCTCCCTGCACCTGCAGTCCCTGCAGGGCATTGGCACAGATGTCTACCTACGGCTCTGCCACATTGATGGCCGGGAGGAA
AGCTTCAGAATC

Alignment

ORF - retro_rnor_2322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MILTSVLGSGPRSGSSLWP-LLGSSLSLRVRSTSATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSVR
          MILTSVLGSGPRSGS.LWP.LLGSSLS.RVRSTSATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSV.
Retrocopy MILTSVLGSGPRSGS*LWP>LLGSSLSFRVRSTSATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSVC

Parental  LTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDF
          LTPTMMLYSG.SQDGSHLLKSG.YLQQEL.VRIAHRIK.FRSLPFIIGCNPTIL.VHELY.R.FQKLTDF
Retrocopy LTPTMMLYSGHSQDGSHLLKSGCYLQQELSVRIAHRIKAFRSLPFIIGCNPTILRVHELYVRVFQKLTDF

Parental  PPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLA
          PPIKDQAD.AQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLV.Y.LDKTL.SRLGIRMLATHHLA
Retrocopy PPIKDQAD*AQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVWYLLDKTLKSRLGIRMLATHHLA

Parental  LHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKN
          LHEDKPDFVGIICTRLSPKKIIEKWVDFAR.LCEHKYGNAPRVRINGHVAA.FPFIPM.LDYILPELLKN
Retrocopy LHEDKPDFVGIICTRLSPKKIIEKWVDFARCLCEHKYGNAPRVRINGHVAAGFPFIPMRLDYILPELLKN

Parental  AMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLF
          A.RATM.SHLDTPYNVPDVVITIA.N.VDLIIRISD.GGGIAH.DLDRVMD.HFTT.EASTQDP.I.PLF
Retrocopy AVRATMGSHLDTPYNVPDVVITIASNVVDLIIRISDQGGGIAHNDLDRVMDHHFTTSEASTQDPQIGPLF

Parental  GHLDMHSGGQSGPMHGFGFG-LPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDGREESFRI
          GHLDMH....SGPMH..GFG.LP...AYAEYL.GSL.LQSLQGIGTDVYLRL.HIDGREESFRI
Retrocopy GHLDMH----SGPMH--GFG<LPV--AYAEYLVGSLHLQSLQGIGTDVYLRLCHIDGREESFRI

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
SRP017611_brain	0.22 RPM	33.07 RPM
SRP017611_kidney	0.07 RPM	112.56 RPM
SRP017611_liver	0.00 RPM	22.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2322 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2322 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000014497	1 retrocopy	retro_etel_614,
Monodelphis domestica	ENSMODG00000001837	1 retrocopy	retro_mdom_1033,
Rattus norvegicus	ENSRNOG00000019485	1 retrocopy	retro_rnor_2322 ,