RetrogeneDB ID: retro_mmus_1949

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:87279024..87279386(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082225
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nudt21
• Ensembl ID: ENSMUSG00000031754
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:MGI Symbol;Acc:MGI:1915469]

Sequence

>retro_mmus_1949
GAAGGGGTTTTGATTGTTCATGAGCACCACCTGCCTGTGTTATTGCTACATCTGGGAACAACTTTCTTCAAATTACCTGG
TAGTGAACCTGACCCAGGAGAAGATGAAGTTGAAGGACTAAAACGCTTAATGACAGAGATATCAGGTCATCCAGATGGAG
TCCTAAAAGACTGGGTCATTGATGACTGCATTGGGAACTAGTGGAGACCAAATTTTGAACATTCTCAGTATTTATATATT
TCACAACATATAACAGAGCCCAAGGAACATAAGAAGTTGTTTCTGGTTCAGCTTTAAGAGGAAGCTTGTTTGTAGTTCCT
AAAAATTACAAGCTGGTAGCTGCACTATTGTTTGAGCTGTAT

Alignment

ORF - retro_mmus_1949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.11 %
• Parental protein coverage: 53.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWR
          EGVLIVHEH.LP.VLLL.LGTTFFKLPG.E..PGEDEVEGLKRLMTEI.G..DGVL.DWVIDDCIGN.WR
Retrocopy EGVLIVHEHHLP-VLLLHLGTTFFKLPGSEPDPGEDEVEGLKRLMTEISGHPDGVLKDWVIDDCIGN*WR

Parental  PNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKA-LFAVPKNYKLVAAPLFELY
          PNFE..QY.YI..HIT.PKEHKKLFLVQL.E.A.LF.VPKNYKLVAA.LFELY
Retrocopy PNFEHSQYLYISQHITEPKEHKKLFLVQL*EEA<LFVVPKNYKLVAALLFELY

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	0.00 RPM	12.90 RPM
SRP007412_cerebellum	0.00 RPM	10.77 RPM
SRP007412_heart	0.00 RPM	3.27 RPM
SRP007412_kidney	0.00 RPM	4.87 RPM
SRP007412_liver	0.00 RPM	3.85 RPM
SRP007412_testis	0.00 RPM	5.17 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1949 was not detected

EST

No EST(s) were mapped for retro_mmus_1949 retrocopy.

TSS

No TSS is located nearby retro_mmus_1949 retrocopy 5' end.

Lab

retro_mmus_1949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1949 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Cavia porcellus	ENSCPOG00000003705	1 retrocopy	retro_cpor_1054,
Felis catus	ENSFCAG00000008669	1 retrocopy	retro_fcat_1843,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Mus musculus	ENSMUSG00000031754	3 retrocopies	retro_mmus_1949 , retro_mmus_1950, retro_mmus_2142,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Otolemur garnettii	ENSOGAG00000014888	2 retrocopies	retro_ogar_1450, retro_ogar_630,
Ochotona princeps	ENSOPRG00000006689	1 retrocopy	retro_opri_637,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tursiops truncatus	ENSTTRG00000013545	1 retrocopy	retro_ttru_1087,