RetrogeneDB ID: retro_mmus_2373

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:84915895..84916834(+)
• Located in intron of: ENSMUSG00000038070

Retrocopy information

• Ensembl ID: ENSMUSG00000083139
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dimt1
• Ensembl ID: ENSMUSG00000021692
• Aliases: Dimt1, 1500031M22Rik, AV111347, Dimt1l
• Description: DIM1 dimethyladenosine transferase 1-like (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913504]

Sequence

>retro_mmus_2373
ATGCCGAAGGCCAAGTCCGCAGCGAGTAGCCGCCGGCGGGATCGTCAAGAGTAGCGCAGGGAGCTGAAGCGAGCTGGAGG
ACTCATGTTCAACACAGGGATCGGACAACACATTTTGAAAAATCCTCTAATTGTTAACAGCATCATCGATAAGGCTGCTT
TAAGACCTACCGATGTGGTGCTGGAAGTTGGGCCTGGGACTGGCAATATGACTGTCAAGCTGTTAGAAAAGGCCAAAAAG
GTAGTTGCCTGTGAACTTGATCCAAGGCTAGTAGCTGAACTTCACAAAAGAGTTCAGGGTACGCCTCTGGCCAGCAAACT
CCAGGTCCTGGTGGGAGATGTACTGAAATCAGATTTGCCATTCTTTGATGCTTGTGTGGCAAACTTGCCTTATCAGATCT
CCTCTCCCTTTGTCTTCAAGTTGCTGCTCCACCGGCCATTTTTCAGATGTGCTATACTCATGTTTCAGAGAGAGTTTGCT
CTTCGATTGGTTGCCAAGCCTGGAGATAAATTATACTGTAGACTCTCCATCAACACACAGCTTTTAGCACACGTGGACCA
TCTAATGAAGGTGGGGAAGAATAACTTCAGACTGCCCCCCAAGGTGGAGTCCAGCGTGGTCAGGATAGAACCTAAGAATC
CGCCACCACCAATCAATTTTCAGGAATGGGACGACTTAGTAAGGATCACTTTTGTTCGGAAAAACAAGACACTGTCCGCT
GCATTCAAATCAAGTGCAGTACAACAACTGTTGGAAAAAAATTACAGAATTCACTGTTCAGTACAGAATACTGTAATATC
AGAAGATTTCAGTATAGCAGATAAAATACAGCATATCCTAACCAGCACAGGTTTCAGTGACAAACGGGCCCGTTCCATGG
ACATAGATGACTTTATCAGGTTGCTACATGGATTCAATGCAGAAGGCATCCACTTCTCC

Alignment

ORF - retro_mmus_2373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKAKSAASSRRRDRQEQRRELKRAGGLMFNTGIGQHILKNPLIVNSIIDKAALRPTDVVLEVGPGTGNM
          MPKAKSAASSRRRDRQE.RRELKRAGGLMFNTGIGQHILKNPLIVNSIIDKAALRPTDVVLEVGPGTGNM
Retrocopy MPKAKSAASSRRRDRQE*RRELKRAGGLMFNTGIGQHILKNPLIVNSIIDKAALRPTDVVLEVGPGTGNM

Parental  TVKLLEKAKKVVACELDPRLVAELHKRVQGTPLASKLQVLVGDVLKSDLPFFDACVANLPYQISSPFVFK
          TVKLLEKAKKVVACELDPRLVAELHKRVQGTPLASKLQVLVGDVLKSDLPFFDACVANLPYQISSPFVFK
Retrocopy TVKLLEKAKKVVACELDPRLVAELHKRVQGTPLASKLQVLVGDVLKSDLPFFDACVANLPYQISSPFVFK

Parental  LLLHRPFFRCAILMFQREFALRLVAKPGDKLYCRLSINTQLLARVDHLMKVGKNNFRPPPKVESSVVRIE
          LLLHRPFFRCAILMFQREFALRLVAKPGDKLYCRLSINTQLLA.VDHLMKVGKNNFR.PPKVESSVVRIE
Retrocopy LLLHRPFFRCAILMFQREFALRLVAKPGDKLYCRLSINTQLLAHVDHLMKVGKNNFRLPPKVESSVVRIE

Parental  PKNPPPPINFQEWDGLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHCSVQNTVIPEDFSIADKIQQIL
          PKNPPPPINFQEWD.LVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHCSVQNTVI.EDFSIADKIQ.IL
Retrocopy PKNPPPPINFQEWDDLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHCSVQNTVISEDFSIADKIQHIL

Parental  TSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS
          TSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS
Retrocopy TSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS

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	0.05 RPM	7.73 RPM
SRP007412_cerebellum	0.17 RPM	6.60 RPM
SRP007412_heart	0.00 RPM	2.74 RPM
SRP007412_kidney	0.04 RPM	2.56 RPM
SRP007412_liver	0.03 RPM	1.80 RPM
SRP007412_testis	0.18 RPM	4.12 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2373 was not detected

EST

No EST(s) were mapped for retro_mmus_2373 retrocopy.

TSS

No TSS is located nearby retro_mmus_2373 retrocopy 5' end.

Lab

retro_mmus_2373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2373 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
Echinops telfairi	ENSETEG00000020059	1 retrocopy	retro_etel_34,
Mus musculus	ENSMUSG00000021692	1 retrocopy	retro_mmus_2373 ,