RetrogeneDB ID: retro_rnor_2170

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:124738253..124739024(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000037974
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mthfd2
• Ensembl ID: ENSRNOG00000010833
• Aliases: None
• Description: bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial [Source:RefSeq peptide;Acc:NP_001102868]

Sequence

>retro_rnor_2170
ATGGCTTCTGTTTCCTTGTCTGCGCTGGCAGTGCGGTTGTTGTGCCTCACGCACGGCTGCCACTCCCGCCTACAGTCCTT
CCACCTGGTGGCAGTACGAAATGAAGCCGTCGTCATTTCTGGAAGGAAGCTGGCCCAGCAGATCAAGCAAGAAGTATGGC
AGGAGGTGGAAGAGTGGGTGGCCTCGGGCAACAAGCGGCCACACCTCACTGTCATTCTGGTTGGTGACAATCCTGCCAGT
CACTCCTATGTTCTCAACAAAACCAGGGCAGCAGCTAAAGTGGGAATCAACAGTGAGTCAATTGTGAAACCAGCCTCAGT
GTCAGAGGAAGAGCTGTTGAATTCAATCAGAACATGGAATGACGATGAGAATGTAGATGGCCTCCTTGTTCAGCTGCCAC
TCCCAAAGCACATTGACGAGAGAAAGATCTGCAATGCTGTTTCTCCTGACAAGGATGTTGATGGCTTTCATGTCATCAAC
GTTGGGCGCATGTGTTTGGACCAGTATTCCATGCTGCCAGCAACGCCATGGGGCGTGTGGGAGATACTCAAGCGAACGGG
CATTCCAACCTTAGGGAAGAATGTGGTAGTGGCTGGCAGGTCCAAAAACGTTGGGATGCCAATTGCAATGCTGCTGCACA
CGGATGGAGCGCACGAGCGGCCTGGGGGTGATGCCACAGTCACAATATCTCATCGGCACACTCCTAAAGAACAGCTGAAG
AAGCACAGGATCCTTGCGGACATTGTGATATCTGGGCATTCCAAACCTCAT

Alignment

ORF - retro_rnor_2170 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.77 %
• Parental protein coverage: 73.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSVSLSALAVRLLRPTHGCHSRLQSFHLAAVRNEAVVISGRKLAQQIKQEVRQEVEEWVASGNKRPHLS
          M.SVSLSALAVRLL..THGCHSRLQSFHL.AVRNEAVVISGRKLAQQIKQEV.QEVEEWVASGNKRPHL.
Retrocopy MASVSLSALAVRLLCLTHGCHSRLQSFHLVAVRNEAVVISGRKLAQQIKQEVWQEVEEWVASGNKRPHLT

Parental  VILVGDNPASHSYVLNKTRAAAEVGINSETIVKPASVSEEELLNSIRTLNDDENVDGLLVQLPLPEHIDE
          VILVGDNPASHSYVLNKTRAAA.VGINSE.IVKPASVSEEELLNSIRT.NDDENVDGLLVQLPLP.HIDE
Retrocopy VILVGDNPASHSYVLNKTRAAAKVGINSESIVKPASVSEEELLNSIRTWNDDENVDGLLVQLPLPKHIDE

Parental  RKICNAVSPDKDVDGFHVINVGRMCLDQYSMLPATPWGVWEILKRTGIPTLGKNVVVAGRSKNVGMPIAM
          RKICNAVSPDKDVDGFHVINVGRMCLDQYSMLPATPWGVWEILKRTGIPTLGKNVVVAGRSKNVGMPIAM
Retrocopy RKICNAVSPDKDVDGFHVINVGRMCLDQYSMLPATPWGVWEILKRTGIPTLGKNVVVAGRSKNVGMPIAM

Parental  LLHTDGAHERPGGDATVTISHRHTPKEQLKKHTILADIVISAAGIPN
          LLHTDGAHERPGGDATVTISHRHTPKEQLKKH.ILADIVIS....P.
Retrocopy LLHTDGAHERPGGDATVTISHRHTPKEQLKKHRILADIVISGHSKPH

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	0.00 RPM	3.45 RPM
SRP017611_kidney	0.00 RPM	1.88 RPM
SRP017611_liver	0.00 RPM	0.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2170 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2170 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017345	2 retrocopies	retro_amel_1098, retro_amel_1584,
Canis familiaris	ENSCAFG00000008716	1 retrocopy	retro_cfam_580,
Callithrix jacchus	ENSCJAG00000017810	3 retrocopies	retro_cjac_2225, retro_cjac_2568, retro_cjac_3078,
Macropus eugenii	ENSMEUG00000013987	4 retrocopies	retro_meug_1468, retro_meug_152, retro_meug_1577, retro_meug_2074,
Pongo abelii	ENSPPYG00000012283	3 retrocopies	retro_pabe_2271, retro_pabe_2729, retro_pabe_3077,
Rattus norvegicus	ENSRNOG00000010833	1 retrocopy	retro_rnor_2170 ,