RetrogeneDB ID: retro_mmus_1902

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:35340408..35340960(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000075391
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Glo1
• Ensembl ID: ENSMUSG00000024026
• Aliases: Glo1, 0610009E22Rik, 1110008E19Rik, 2510049H23Rik, AW550643, GLY1, Glo-1, Glo-1r, Glo-1s, Glo1-r, Glo1-s, Qglo
• Description: glyoxalase 1 [Source:MGI Symbol;Acc:MGI:95742]

Sequence

>retro_mmus_1902
ATGGCAGAACCACAGCCGGCGTCCAGTGGCCTCACTGATGAGACCGCTTTCAGCTGCTGCTCCGATCCAGACCCCAGCAC
CAAGGATTTTCTACTGCAGCAAACGATGCTAAGAATTAAGGATCCTAAGAAGTCCCTGGATTTTTATACGAGGGTTCTTG
GACTGACCCTCCTGCAGAAGCTTGACTTCCCTGCTATGAAGTTCTCGCTCTACTTCTTAGCTTACGAGGATAAGAACGAT
ATCCCCAAGGACAAGTCCGAGAAGACAGCATGGACGTTTTCCAGAAAAGCCACCCTTGAGCTCACGCACAACTGGGGCAC
TGAAGATGACGAGACTCAGAGTTACCACAACGGCAACTCGGACCCTCGTGGATTTGGTCACATTGGGATTGCCGTTCCTG
ATGTCTACAGTGCCTGTAAGAGATTTGAAGAACTAGGTGTCAAGTTTGTGAAGAAGCCTGATGACGGGAAAATGAAAGGA
CTGGCGTTCATTCAAGACCCTGACGGCTACTGGATTGAGATTCTGAATCCTAACAAAATAGCAACGATTATT

Alignment

ORF - retro_mmus_1902 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAEPQPASSGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSL
          MAEPQPASSGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSL
Retrocopy MAEPQPASSGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSL

Parental  YFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACK
          YFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACK
Retrocopy YFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACK

Parental  RFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATII
          RFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATII
Retrocopy RFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATII

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	1.61 RPM	56.70 RPM
SRP007412_cerebellum	3.86 RPM	103.99 RPM
SRP007412_heart	0.12 RPM	46.70 RPM
SRP007412_kidney	3.39 RPM	97.69 RPM
SRP007412_liver	12.78 RPM	228.19 RPM
SRP007412_testis	1.05 RPM	19.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1902 was not detected

EST

No EST(s) were mapped for retro_mmus_1902 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_86769	408 libraries	72 libraries	335 libraries	154 libraries	103 libraries

The graphical summary, for retro_mmus_1902 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_1902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1902 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012703	2 retrocopies	retro_btau_1003, retro_btau_1513,
Cavia porcellus	ENSCPOG00000010050	1 retrocopy	retro_cpor_1482,
Dasypus novemcinctus	ENSDNOG00000019598	6 retrocopies	retro_dnov_1016, retro_dnov_1064, retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
Dipodomys ordii	ENSDORG00000006369	1 retrocopy	retro_dord_21,
Macropus eugenii	ENSMEUG00000005978	1 retrocopy	retro_meug_1641,
Mus musculus	ENSMUSG00000024026	1 retrocopy	retro_mmus_1902 ,
Otolemur garnettii	ENSOGAG00000007945	2 retrocopies	retro_ogar_2541, retro_ogar_681,
Rattus norvegicus	ENSRNOG00000000541	2 retrocopies	retro_rnor_1012, retro_rnor_1024,
Sus scrofa	ENSSSCG00000027778	1 retrocopy	retro_sscr_853,
Ictidomys tridecemlineatus	ENSSTOG00000005821	1 retrocopy	retro_itri_1626,
Tupaia belangeri	ENSTBEG00000014386	1 retrocopy	retro_tbel_4376,
Tursiops truncatus	ENSTTRG00000004664	1 retrocopy	retro_ttru_90,