RetrogeneDB ID: retro_mmus_907

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:115892883..115893759(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Uevld
• Ensembl ID: ENSMUSG00000043262
• Aliases: Uevld, 8430408E05Rik, Attp
• Description: UEV and lactate/malate dehyrogenase domains [Source:MGI Symbol;Acc:MGI:1860490]

Sequence

>retro_mmus_907
ATGGAGTTCGACTGTGAGGGCGTGAGATGGCTGCTAGGCAAGTACAAGTTCAGGGATCTGACTGTGGAAGAGCTGAAGAA
TGTGAGCGTGTCTTTCCCGCACTTCAGATACTCCGTGGACACCTATGTTTTCAAAGATACATCCCAAAAAGACCTGCTGA
ATTTCACCGGTACAATTCCTGTGATGTATCAGGGTAAGACATACAACATACCCATTCGCTTCTGGATTTTGGATTCCCAC
CCTTTTGCTCCACCCATTTGCTTCTTGAAGCCAACTGCAAACATGGAAATCTCGGTTGGAAAACATGTGGATGCCAAAGG
CAGAATATACTTGCCCTATCACCAAAACTGGAGCCACCCCAAATCTGCCATCGTTGGATTAATTAAAGAAATGATTGCCA
AGTTTCAAGAGGAACTTCCTCTCTATTCCATATCGTCGTCCAATGAAGCGCAACAGGTGGACTTGCTGGCCTATATCACA
AAAATCATGGAAGGTGTCTCAGACATAAATTCAAGGGGCTGGACAAATCATGAGAATAAAATACTCAATAAAATCACTGT
GGTTGGAAGTGGAGATTTGGGTATCGCCTGCACATTGGCAATTTCAGCAAAGGGCATTGCAGACAAGCTGCTCCTCTTAG
ACCTCTCAGACGGGATGAGCCAAGGGACAATGGACCTTGATATCTTCAACCTGCCTAATGTAGAGATCAGCAAAGATTTG
TCTGCCTCTGCTCATTCCAAGGTGGTGATCTTCACAGCCAACTCTTTGGGCGGTTCTGAATCCTATCTGCATGCAGTACA
AAGTAATGTGGACATGTTCAGAGCTCTTGTTCCAGCTCTGGGACACTATAGTCAACACGCTGTCTTGCTTGTTGCC

Alignment

ORF - retro_mmus_907 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.63 %
• Parental protein coverage: 62. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEFDCEGVRRLLGKYKFRDLTVEELKNVSVSFPHFRYSVDTYVFKDTSQKDLLNFTGTIPVMYQGKTYNI
          MEFDCEGVR.LLGKYKFRDLTVEELKNVSVSFPHFRYSVDTYVFKDTSQKDLLNFTGTIPVMYQGKTYNI
Retrocopy MEFDCEGVRWLLGKYKFRDLTVEELKNVSVSFPHFRYSVDTYVFKDTSQKDLLNFTGTIPVMYQGKTYNI

Parental  PIRFWILDSHPFAPPICFLKPTANMEISVGKHVDAKGRIYLPYLQNWSHPKSAIVGLIKEMIAKFQEELP
          PIRFWILDSHPFAPPICFLKPTANMEISVGKHVDAKGRIYLPY.QNWSHPKSAIVGLIKEMIAKFQEELP
Retrocopy PIRFWILDSHPFAPPICFLKPTANMEISVGKHVDAKGRIYLPYHQNWSHPKSAIVGLIKEMIAKFQEELP

Parental  LYSIPSSNEAQQVDLLAYITKITEGVSDINSRGWTNHENKILNKITVVGSGDLGIACTLAISAKGIADKL
          LYSI.SSNEAQQVDLLAYITKI.EGVSDINSRGWTNHENKILNKITVVGSGDLGIACTLAISAKGIADKL
Retrocopy LYSISSSNEAQQVDLLAYITKIMEGVSDINSRGWTNHENKILNKITVVGSGDLGIACTLAISAKGIADKL

Parental  LLLDLSDGMSQGTMDLDIFNLPNVEISKDLSASAHSKVVIFTANSLGGSESYLHAVQSNVDMFRALVPAL
          LLLDLSDGMSQGTMDLDIFNLPNVEISKDLSASAHSKVVIFTANSLGGSESYLHAVQSNVDMFRALVPAL
Retrocopy LLLDLSDGMSQGTMDLDIFNLPNVEISKDLSASAHSKVVIFTANSLGGSESYLHAVQSNVDMFRALVPAL

Parental  GHYSQHAVLLVA
          GHYSQHAVLLVA
Retrocopy GHYSQHAVLLVA

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
SRP007412_brain	0.07 RPM	7.94 RPM
SRP007412_cerebellum	0.17 RPM	7.25 RPM
SRP007412_heart	0.09 RPM	4.79 RPM
SRP007412_kidney	0.23 RPM	5.58 RPM
SRP007412_liver	0.08 RPM	5.05 RPM
SRP007412_testis	0.14 RPM	3.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_907 was not detected

EST

No EST(s) were mapped for retro_mmus_907 retrocopy.

TSS

No TSS is located nearby retro_mmus_907 retrocopy 5' end.

Lab

retro_mmus_907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_907 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000003117	1 retrocopy	retro_mmur_1485,
Mus musculus	ENSMUSG00000030246	4 retrocopies	retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Mus musculus	ENSMUSG00000043262	1 retrocopy	retro_mmus_907 ,
Mus musculus	ENSMUSG00000063229	14 retrocopies	retro_mmus_1044, retro_mmus_1300, retro_mmus_1514, retro_mmus_1608, retro_mmus_1753, retro_mmus_1887, retro_mmus_1889, retro_mmus_1925, retro_mmus_2078, retro_mmus_2592, retro_mmus_2885, retro_mmus_3150, retro_mmus_3694, retro_mmus_497,