RetrogeneDB ID: retro_mmus_2711

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:149155448..149156201(-)
• Located in intron of: ENSMUSG00000097191

Retrocopy information

• Ensembl ID: ENSMUSG00000024437
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gnpda1
• Ensembl ID: ENSMUSG00000052102
• Aliases: Gnpda1, GNPDA, Gnp1, Gnpi, oscillin
• Description: glucosamine-6-phosphate deaminase 1 [Source:MGI Symbol;Acc:MGI:1347054]

Sequence

>retro_mmus_2711
CTGGATGAGGGGAGCACCCCGCTTGGCTGCTACCAGAAGCTGATTGAGTACTATAAGAATGGGGACCTGTCCTTTCAATA
TGTGAAAACCTTCAACATGGACGAGTATGTGGGTCTTCCTCGAGACCACCCAGAGAGTTACCACTCCTTCATGTGGAATA
ATTTCTTCAAGCACATTGACATCCACCCCGAAAACACCCACATTTTGGATGGAAATGCGGCTGACCTGCAGGCCGAGTGT
GATGCCTTTGAGGAGAAGATCCAGGCTGCCGGAGGGATCGAACTCTTTGTCGGAGGCATTGGCCCCGATGGACACATTGC
CTTCAATGAGCCAGGCTCCAGCCTGGTGTCCAGGACCCGTGTGAAGACTCTGGCTATGGACACCATCCTGGCCAACGCTA
GGTTCTTTGATGGTGATCTTGCCAAGGTGCCCACCATGGCCCTAACAGTGGGGGTCGGCACTGTCATGGATGCTAAAGAG
GTGATGATCCTCATCACAGGCGCTCACAAGGCCTTCGCTCTGTACAAAGCCATCGAGGAGGGTGTGAACCACATGTGGAC
GGTGTCCGCCTTTCAGCAGCACCCCCGCACTGTGTTTGTGTGTGACGAGGACGCCACCTTGGAACTAAAAGTGAAGACAG
TCAAATATTTCAAAGGTTTAATGCTTGTTCATAACAAGCTGGTGGACCCCCTGTACAGTATCAAGGAGAAGGAAATTCAG
AAAAGCCAATCTGCTAAGAAGCCATACAGTGAC

Alignment

ORF - retro_mmus_2711 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.2 %
• Parental protein coverage: 86.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPTGSTPLGCYQKLIEYYKNGDLSFQYVKTFNMDEYVGLPRDHPESYHSFMWNNFFKHIDIHPENTHILD
          L..GSTPLGCYQKLIEYYKNGDLSFQYVKTFNMDEYVGLPRDHPESYHSFMWNNFFKHIDIHPENTHILD
Retrocopy LDEGSTPLGCYQKLIEYYKNGDLSFQYVKTFNMDEYVGLPRDHPESYHSFMWNNFFKHIDIHPENTHILD

Parental  GNAADLQAECDAFEEKIQAAGGIELFVGGIGPDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGDL
          GNAADLQAECDAFEEKIQAAGGIELFVGGIGPDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGDL
Retrocopy GNAADLQAECDAFEEKIQAAGGIELFVGGIGPDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGDL

Parental  AKVPTMALTVGVGTVMDAKEVMILITGAHKAFALYKAIEEGVNHMWTVSAFQQHPRTVFVCDEDATLELK
          AKVPTMALTVGVGTVMDAKEVMILITGAHKAFALYKAIEEGVNHMWTVSAFQQHPRTVFVCDEDATLELK
Retrocopy AKVPTMALTVGVGTVMDAKEVMILITGAHKAFALYKAIEEGVNHMWTVSAFQQHPRTVFVCDEDATLELK

Parental  VKTVKYFKGLMLVHNKLVDPLYSIKEKEIQKSQSAKKPYSD
          VKTVKYFKGLMLVHNKLVDPLYSIKEKEIQKSQSAKKPYSD
Retrocopy VKTVKYFKGLMLVHNKLVDPLYSIKEKEIQKSQSAKKPYSD

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	0.28 RPM	9.18 RPM
SRP007412_cerebellum	0.43 RPM	4.73 RPM
SRP007412_heart	0.06 RPM	7.75 RPM
SRP007412_kidney	1.19 RPM	31.97 RPM
SRP007412_liver	0.55 RPM	7.62 RPM
SRP007412_testis	0.59 RPM	6.86 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2711 was not detected

EST

No EST(s) were mapped for retro_mmus_2711 retrocopy.

TSS

No TSS is located nearby retro_mmus_2711 retrocopy 5' end.

Lab

retro_mmus_2711 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2711 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007865	1 retrocopy	retro_btau_535,
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278, retro_chof_42,
Dasypus novemcinctus	ENSDNOG00000007804	3 retrocopies	retro_dnov_1363, retro_dnov_1608, retro_dnov_508,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Mus musculus	ENSMUSG00000052102	1 retrocopy	retro_mmus_2711 ,
Otolemur garnettii	ENSOGAG00000007303	3 retrocopies	retro_ogar_2251, retro_ogar_2506, retro_ogar_446,
Ictidomys tridecemlineatus	ENSSTOG00000016508	1 retrocopy	retro_itri_1135,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431, retro_tbel_59,