RetrogeneDB ID: retro_mmus_2701

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:138364262..138365552(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080935
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Got2
• Ensembl ID: ENSMUSG00000031672
• Aliases: Got2, AL022787, FABP-pm, Got-2, mAspAT
• Description: glutamate oxaloacetate transaminase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:95792]

Sequence

>retro_mmus_2701
ATGGCCCTCCTGCACTCCAGCCGCATCCTCTCCGGGATGGCTGCTGCCTTTCACCCAGGCCTAGCTGCTGCAGCCTCTGC
CAGAGCCAGCTCCTGGTGGACCCATGTCGAAATGGGACCTCCAGATCCCATCCTGGGCGTTACCGAAGCCTTCAAGAGAG
ATACCAACAGCAAGAAGATGAACCTGGGAGTTGGTGCCTACCGGGATGATAACGGAAAACCTTACGTGCTCCCCAGTGTC
CGGAAGGCAGAGGCCCAGATTGCTGCAAAAAATTTGGACAAGGAATACCTGCCCATTGGGGGACTGGCTGAATTCTGTAA
GGCTTCTGCAGAACTGGCCCTGGGCGAGAACAACGAAGTGTTGAAAAGCGGCCGGTTCGTCACTGTGCAGACCATTTCCG
GGACTGGAGCCTTAAGGGTCGGGGCCAGTTTTCTGCAAAGGTTTTTTAAGTTCAGCCAAGATGTCTTTCTGCCCAAACCG
TCCTGGGGGAATCACACGCCCATCTTCAGGGATGCCGGCATGCAGCTCCAAGGTTATCGCTACTATGACCCCAAGACTTG
CGGTTTTGACTTCTCCGGAGCCCTAGAAGACATATCAAAAATCCCAGAGCAGAGTGTCCTCCTCCTGCATGCCTGCGCTC
ACAACCCCACAGGCGTGGACCCTCGTCCCGAGCAGTGGAAGGAGATAGCGTCCGTGGTGAAGAAAAAGAATCTCTTCGCA
TTCTTTGACATGGCCTACCAAGGCTTTGCCAGCGGTGATGGTGATAAGGATGCCTGGGCCGTGCGGCACTTCATCGAGCA
GGGCATCAATGTCTGCCTCTGCCAATCGTATGCCAAGAACATGGGCCTGTACGGTGAGCGTGTGGGAGCCTTCACGGTGG
TCTGCAAAGATGCAGAAGAAGCCAAAAGGGTGGAGTCACAGCTGAAGATCTTGATCCGTCCCCTGTATTCCAACCCACCT
CTCAATGGGGCCCGGATCACAGCAACCATCCTGACTTCTCCAGACTTGCGGAAGCAATGGTTGCAAGAGGTGAAAGGCAT
GGCTGACCGCATCATCAGCATGAGGACCCAGCTGGTCTCCAACCTGAAGAAAGAGGGCTCTTCCCACAACTGGCAGCACA
TCACCGACCAGATCGGCATGTTCTGTTTCACCGGCCTAAAGCCAGAGCAGGTGGAGCGGCTGACCAAGGAGTTCTCGGTC
TACATGACAAAGGATGGCCGAATCTCCGTGGCAGGGGTCACCTCTGGCAATGTGGGCTACCTTGCCCATGCCATTCACCA
GGTCACCAAG

Alignment

ORF - retro_mmus_2701 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALLHSSRILSGMAAAFHPGLAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDD
          MALLHSSRILSGMAAAFHPGLAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDD
Retrocopy MALLHSSRILSGMAAAFHPGLAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDD

Parental  NGKPYVLPSVRKAEAQIAAKNLDKEYLPIGGLAEFCKASAELALGENNEVLKSGRFVTVQTISGTGALRV
          NGKPYVLPSVRKAEAQIAAKNLDKEYLPIGGLAEFCKASAELALGENNEVLKSGRFVTVQTISGTGALRV
Retrocopy NGKPYVLPSVRKAEAQIAAKNLDKEYLPIGGLAEFCKASAELALGENNEVLKSGRFVTVQTISGTGALRV

Parental  GASFLQRFFKFSRDVFLPKPSWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFSGALEDISKIPEQSVLLLH
          GASFLQRFFKFS.DVFLPKPSWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFSGALEDISKIPEQSVLLLH
Retrocopy GASFLQRFFKFSQDVFLPKPSWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFSGALEDISKIPEQSVLLLH

Parental  ACAHNPTGVDPRPEQWKEIASVVKKKNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSYAKN
          ACAHNPTGVDPRPEQWKEIASVVKKKNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSYAKN
Retrocopy ACAHNPTGVDPRPEQWKEIASVVKKKNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSYAKN

Parental  MGLYGERVGAFTVVCKDAEEAKRVESQLKILIRPLYSNPPLNGARIAATILTSPDLRKQWLQEVKGMADR
          MGLYGERVGAFTVVCKDAEEAKRVESQLKILIRPLYSNPPLNGARI.ATILTSPDLRKQWLQEVKGMADR
Retrocopy MGLYGERVGAFTVVCKDAEEAKRVESQLKILIRPLYSNPPLNGARITATILTSPDLRKQWLQEVKGMADR

Parental  IISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSVYMTKDGRISVAGVTSGNVGY
          IISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSVYMTKDGRISVAGVTSGNVGY
Retrocopy IISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSVYMTKDGRISVAGVTSGNVGY

Parental  LAHAIHQVTK
          LAHAIHQVTK
Retrocopy LAHAIHQVTK

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	0.21 RPM	100.69 RPM
SRP007412_cerebellum	0.09 RPM	86.89 RPM
SRP007412_heart	1.99 RPM	404.19 RPM
SRP007412_kidney	1.04 RPM	208.24 RPM
SRP007412_liver	0.55 RPM	224.07 RPM
SRP007412_testis	0.59 RPM	4.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2701 was not detected

EST

No EST(s) were mapped for retro_mmus_2701 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_111257	735 libraries	286 libraries	45 libraries	5 libraries	1 library

The graphical summary, for retro_mmus_2701 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_2701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2701 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Mus musculus	ENSMUSG00000031672	1 retrocopy	retro_mmus_2701 ,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,