RetrogeneDB ID: retro_mmus_237

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:5639583..5640996(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000043192
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Gpi1
• Ensembl ID: ENSMUSG00000036427
• Aliases: None
• Description: glucose phosphate isomerase 1 [Source:MGI Symbol;Acc:MGI:95797]

Sequence

>retro_mmus_237
CTGCGCTCACCCGGAACCCGCAGTTCCAGAAGCTGCTGGAGTGGCACCAACCTCAAGCTGCGCGAACTTTTTGAGGCGGA
TCCGGAGCGCTTCAACAACTTCAGCTTGAACCTCAACACCAACCATGGGCATATTCTGGTGGACTACTCCAAGAACCTTG
TGAACAAGGAGGTGATGCAAATGCTGGTGGAGCTGGCCAAGTCCAGAGGTGTGGAGGCTGCACGGGACAACATGTTCAGT
GGTTCCAAGATCAACTACACCGAGGATCGGGCGGTGCTGCATGTGGCCCTTCGGAACCGGTCCAACACACCCATCAAGGT
GGTCGGGAAAGATGTGATGCCGGAGGTGAACAGGGTTCTGGACAAGATGAAGTCTTTCTGCCAGACCTTGACCACCCAGG
AGACCATCACCAATGCAGAGACAGCAAAGGAGTGGTTTCTCGAAGCAGCCAAGGATCCATCTGCAGTTGCAAAGCACTTT
GTCGCCCTGTCTACGAACACGGCCAAAGTGAAAGAGTTTGGAATTGACCCTCAAAACATGTTCGAGTTCTGGGATTGGGT
AGGTGGCCGCTATTCGCTGTGGTCAGCCACTGGACCTTCCATTGCTCTGCATGTAGGTTTTGACCACTTCGAGCAGCTGC
TGTCCGGGGCTCACTGGATGGACCAGCACTTCCTCAAGACGCCCCTAGAGAAGAATGCCCCCGTCCTGCTGGCTCTACTG
GGCATCTGGTACATCAACTGCTACGGTTGTGAGACCCACGCCTTGCTGCCCTATGACCAGTACATGTACCGCTTTGCTGC
CTATTTCCAGCAGGGTGACATGGAGTCCAACGGAAAGTACATCACCAAGTCCGGGGCCCGCGTGGACCACCAGACAGGCC
CCATCGTGTGGGGGGAACCAGGGACCAATGGTCAACACGCATTCTACCAGCTCATCCACCAAGGCACCAAGATGATACCC
TGTGACTTTCTCATCCCTGTCCAGACCCAGCACCCCATACGGAAAGGTCTACATCACAAGATCCTCCTGGCTAACTTCTT
GGCCCAGACTGAGGCCCTGATGATGGGGAAGTTGCCTGAAGAGGCCAGGAAGGAGCTCCAGGCTGCCGGAAAGAGCCCAG
AAGACTTGGAGAAACTCTTGCCACACAAGGTCTTTGAAGGAAACCGCCCGACCAACTCTATTGTGTTTACCAAGCTAACA
CCCTTCATTCTGGGGGCCTTGATTGCCATGTATGAGCACAAGATCTTTGTTCAGGGCATCATGTGGGACATCAACAGCTT
TGACCAGTGGGGAGTGGAGCTGGGGAAGCAGCTGGCCAAGAAAATTGAGCCGGAGCTGGAGGGCAGCTCTGCTGTGACCT
CCCATGATTCCTCCACTAACGGACTGATCAGCTTCATCAAGCAACAGTGGGAC

Alignment

ORF - retro_mmus_237 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.97 %
• Parental protein coverage: 61.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTFTTQETITNAETAKEWFLEAAKDPSAVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAI
          .T.TTQETITNAETAKEWFLEAAKDPSAVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSA.
Retrocopy QTLTTQETITNAETAKEWFLEAAKDPSAVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAT

Parental  GLSIALHVGFDHFEQLLSGAHWMDQHFLKTPLEKNAPVLLALLGIWYINCYGCETHALLPYDQYMHRFAA
          G.SIALHVGFDHFEQLLSGAHWMDQHFLKTPLEKNAPVLLALLGIWYINCYGCETHALLPYDQYM.RFAA
Retrocopy GPSIALHVGFDHFEQLLSGAHWMDQHFLKTPLEKNAPVLLALLGIWYINCYGCETHALLPYDQYMYRFAA

Parental  YFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGL
          YFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGL
Retrocopy YFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGL

Parental  HHKILLANFLAQTEALMKGKLPEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILGAL
          HHKILLANFLAQTEALM.GKLPEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILGAL
Retrocopy HHKILLANFLAQTEALMMGKLPEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILGAL

Parental  IAMYEHKIFVQGIMWDINSFDQWGVELGKQLAKKIEPELEGSSAVTSHDSSTNGLISFIKQQRD
          IAMYEHKIFVQGIMWDINSFDQWGVELGKQLAKKIEPELEGSSAVTSHDSSTNGLISFIKQQ.D
Retrocopy IAMYEHKIFVQGIMWDINSFDQWGVELGKQLAKKIEPELEGSSAVTSHDSSTNGLISFIKQQWD

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	1.45 RPM	375.42 RPM
SRP007412_cerebellum	0.96 RPM	386.67 RPM
SRP007412_heart	1.87 RPM	424.62 RPM
SRP007412_kidney	1.35 RPM	375.27 RPM
SRP007412_liver	0.46 RPM	158.36 RPM
SRP007412_testis	1.83 RPM	368.38 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_237 was not detected

EST

No EST(s) were mapped for retro_mmus_237 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_142796	63 libraries	213 libraries	206 libraries	135 libraries	455 libraries
TSS #2	TSS_142797	288 libraries	144 libraries	48 libraries	130 libraries	462 libraries

The graphical summary, for retro_mmus_237 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_237 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007303	3 retrocopies	retro_cfam_1715, retro_cfam_1935, retro_cfam_2101,
Cavia porcellus	ENSCPOG00000008562	1 retrocopy	retro_cpor_983,
Macropus eugenii	ENSMEUG00000010190	4 retrocopies	retro_meug_1022, retro_meug_1281, retro_meug_559, retro_meug_991,
Microcebus murinus	ENSMICG00000011620	1 retrocopy	retro_mmur_1496,
Myotis lucifugus	ENSMLUG00000003037	1 retrocopy	retro_mluc_444,
Macaca mulatta	ENSMMUG00000005880	1 retrocopy	retro_mmul_2086,
Mustela putorius furo	ENSMPUG00000007520	1 retrocopy	retro_mputfur_1370,
Mus musculus	ENSMUSG00000036427	1 retrocopy	retro_mmus_237 ,