RetrogeneDB ID: retro_mmus_3696

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:121334990..121336574(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083668
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Uhrf1
• Ensembl ID: ENSMUSG00000001228
• Aliases: Uhrf1, AL022808, ICBP90, Np95, RNF106
• Description: ubiquitin-like, containing PHD and RING finger domains, 1 [Source:MGI Symbol;Acc:MGI:1338889]

Sequence

>retro_mmus_3696
AACATCAGGCTCTTGAATGACTCTCAGCTCAACAACTGTCGGATCATGTTTGTGGATGAAGTCTTGATGATTGAGCTCCC
TAATGAGAGGAGGCCTTTGATCGCTAGCCCCTCGCAACCCCCTCCTGCCCTCCGGAACACAGGGAAGAGTGGCCCATCCT
GCCGGTTCTGCAAGGATGATGAAAACAAACCATGTCGAAAGTGTGCCTGCCACGTGTGTGGTGGGCGCGAGGCTCCTGAG
AAACAGCTGTTGTGTGATGACTGTGACATGGCCTTCCACCTGTACTGCCTGAAGCCACCGCTCACCTCTGTCCCCCCTGA
GCCGGAGTGGTACTGCCCCAGCTGCCGCACTGACTCAAGTGAGGTGGTACAAGCAGGGGAGCTGAAGGAGAACAAGAAGA
AGGCAAAGATGGCATCAGCCACTTCCTCCTCCCAGCGGGACTGGGGTAAGGGCATGGCATGTGTGGGCCGCACCACAGAG
TGTACCATTGTGCCCGCCAACCACTTTGGGCCCATCCCTGGTGTCCCTGTGGGCACCATGTGGCACTTCAGAGTCCAGGT
CAGTGAGTCCGGTGTGCATCGGCCTCATGTGGCAGGCATCCATGGCCGGAGCAACGACGGTGCCTACTCATTGGTCCTGG
CTGGTGGCTATGAGAATGATGTGGACAATGGCAATTACTTCACATACACAGGGAGTGGTGGCCGAGACCTCTCTGGCAAC
AAGCGTACAGCAGGCCAGTCCTCTGACCAGAAGCTCACTAATAACAATAGGGCTCTGGCACTCAATTGCCACTCCCCAAT
CAATGAGAAAGGTGCGGAGGCTGAAGACTGGCGCCAAGGGAAGCCAGTGTGTGTGGTCCGGAACATGAAGGGCGGGAAAC
ACAGCAAGTACGCTCCCGCAGAGGGCAACCGCTATGATGGCATCTACAAGGTGGTGAAGTACTGGCCAGAGAGAGGGAAA
TCTGGCTTCCTCATGTGGCATTATCTCCTTCGACGAGATGACACAGAGCCTGAGCCCTGGACCCGAAAGGGCAAGGACCG
CACTCGACAGCTGGGGCTCACTATGCAGTACCCTGAAGGCTACTTGGAGGCCTTGGCTAACAAGGAGAAGAGCAGGAAGC
GCCCGGCCAAGGCCTTGGAGCAGGGACCCTCATCTTCCAAGACAGGCAAAAGCAAACAGAAATCCACAGGGCCAACCCTC
TCCAGCCCCCGTGCCTCTAAGAATAGCAAGCTGGAGCCATACACACTCTCAGAGCAGCAGGCTAACCTCATCAAAGAGGA
CAAGGGCAACGCCAAGCTGTGGGATGATGTGCTAACTTCACTTCAGGATGGGCCGTACCAGATCTTCCTGAGCAAGGTGA
AAGAGGCTTTCCAGTGCATCTGCTGCCAGGAGCTGGTGTTCCGGCCAGTAACCACCGTGTGTCAGCACAACGTCTGTAAG
GACTGTCTGGACAGGTCCTTACGGGCCCAGGTGTTCAGCTGCCCAGCCTGTGGCTATGAGCTGGACCACAGCTCCCCAAC
CCGGGTGAACCAGCCCTTGCAGACCATTCTCAACCAGCTCTTCCCTGGCTATGGCAGCGGCCGG

Alignment

ORF - retro_mmus_3696 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.16 %
• Parental protein coverage: 67.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NIRLLNDSQLNNCRIMFVDEVLMIELPKERRPLIASPSQPPPALRNTGKSGPSCRFCKDDENKPCRKCAC
          NIRLLNDSQLNNCRIMFVDEVLMIELP.ERRPLIASPSQPPPALRNTGKSGPSCRFCKDDENKPCRKCAC
Retrocopy NIRLLNDSQLNNCRIMFVDEVLMIELPNERRPLIASPSQPPPALRNTGKSGPSCRFCKDDENKPCRKCAC

Parental  HVCGGREAPEKQLLCDECDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGEKLKESKKKAKMAS
          HVCGGREAPEKQLLCD.CDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGE.LKE.KKKAKMAS
Retrocopy HVCGGREAPEKQLLCDDCDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGE-LKENKKKAKMAS

Parental  ATSSSRRDWGKGMACVGRTTECTIVPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAY
          ATSSS.RDWGKGMACVGRTTECTIVPANHFGPIPGVPVGTMW.FRVQVSESGVHRPHVAGIHGRSNDGAY
Retrocopy ATSSSQRDWGKGMACVGRTTECTIVPANHFGPIPGVPVGTMWHFRVQVSESGVHRPHVAGIHGRSNDGAY

Parental  SLVLAGGYEDDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQ
          SLVLAGGYE.DVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQ
Retrocopy SLVLAGGYENDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQ

Parental  GKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKDRTR
          GKPV.VVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFL.W.YLLRRDDTEPEPWTR.GKDRTR
Retrocopy GKPVCVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLMWHYLLRRDDTEPEPWTRKGKDRTR

Parental  QLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRASKKSKLEPYTLSEQ
          QLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRASK.SKLEPYTLSEQ
Retrocopy QLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRASKNSKLEPYTLSEQ

Parental  QANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELVFRPVTTVCQHNVCKDCLDRSFRA
          QANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELVFRPVTTVCQHNVCKDCLDRS.RA
Retrocopy QANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELVFRPVTTVCQHNVCKDCLDRSLRA

Parental  QVFSCPACRFELDHSSPTRVNQPLQTILNQLFPGYGSGR
          QVFSCPAC..ELDHSSPTRVNQPLQTILNQLFPGYGSGR
Retrocopy QVFSCPACGYELDHSSPTRVNQPLQTILNQLFPGYGSGR

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	1.17 RPM
SRP007412_cerebellum	0.00 RPM	0.48 RPM
SRP007412_heart	0.00 RPM	1.90 RPM
SRP007412_kidney	0.00 RPM	3.77 RPM
SRP007412_liver	0.00 RPM	0.85 RPM
SRP007412_testis	0.41 RPM	102.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3696 was not detected

EST

No EST(s) were mapped for retro_mmus_3696 retrocopy.

TSS

No TSS is located nearby retro_mmus_3696 retrocopy 5' end.

Lab

retro_mmus_3696 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3696 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000001228	1 retrocopy	retro_mmus_3696 ,
Nomascus leucogenys	ENSNLEG00000013406	1 retrocopy	retro_nleu_1267,