RetrogeneDB ID: retro_mmus_2142

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:21049564..21050245(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000039617
• 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_2142
ATGTCTGTGGTGCCGCCCAATCGCTCGCAGACGGGCTGGCCCCGGGGGGTCAACCAGTTCGGCAACAAGTACATCCAGCA
GACCAAGCCCCTCACCCTGGAGCGCACCATTAATCTGTACCCGCTTACCAATTATACTTTTGGTACAAAGGAGCCCCTCT
ATGAGAAGGACAGCTCTGTTGCAGCCAGATTTCAGCGCATGAGGGAGGAATTTGATAAGATTGGGATGAGAAGGACTGTA
GAAGGGGTTCTGATTGTTCATGAACACCGCCTGCCCCACGTGCTCCTGCTGCAGCTGGGGACAACTTTCTTCAAATTACC
TGGTGGGGAACTTAACCCAGGAGAAGATGAAGTTGAAGGACTAAAACGCTTAATGACAGAGATACTTGGTCGTCAAGATG
GAGTCCTGCAAGACTGGGTCATTGATGACTGCATTGGGAACTGGTGGAGACCAAATTTTGAACCTCCTCAGTATCCGTAT
ATTCCTGCACATATAACAAAACCCAAGGAACATAAGAAGTTGTTTCTGGTTCAGCTTCAAGAGAAAGCCTTGTTTGCAGT
CCCTAAAAATTACAAGCTGGTAGCTGCACCATTGTTTGAGCTGTATGACAATGCACCGGGGTATGGACCCATCATTTCTA
GTCTTCCTCAGCTGCTGAGCAGGTTCAATTTTATATACAAC

Alignment

ORF - retro_mmus_2142 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  MSVVPPNRSQTGWPRGVNQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREE
          MSVVPPNRSQTGWPRGVNQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREE
Retrocopy MSVVPPNRSQTGWPRGVNQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREE

Parental  FDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWV
          FDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWV
Retrocopy FDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWV

Parental  IDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP
          IDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP
Retrocopy IDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP

Parental  IISSLPQLLSRFNFIYN
          IISSLPQLLSRFNFIYN
Retrocopy IISSLPQLLSRFNFIYN

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	0.07 RPM	12.90 RPM
SRP007412_cerebellum	0.00 RPM	10.77 RPM
SRP007412_heart	0.09 RPM	3.27 RPM
SRP007412_kidney	0.06 RPM	4.87 RPM
SRP007412_liver	0.00 RPM	3.85 RPM
SRP007412_testis	0.14 RPM	5.17 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2142 was not detected

EST

1 EST(s) were mapped to retro_mmus_2142 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI157777	21049907	21050073	98.8	164	2	162

TSS

No TSS is located nearby retro_mmus_2142 retrocopy 5' end.

Lab

retro_mmus_2142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2142 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,