RetrogeneDB ID: retro_mmus_2542

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:7857107..7857844(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081226
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lin37
• Ensembl ID: ENSMUSG00000036845
• Aliases: Lin37, 1810054G18Rik
• Description: lin-37 homolog (C. elegans) [Source:MGI Symbol;Acc:MGI:1922910]

Sequence

>retro_mmus_2542
ATGTTCCCGGTAAAGGTGAAAGTGGAGAAATCAGAGATGGAGATGGCCAAAGCCCGGAACCAGCTGGATGCCGTTCTTCA
GTGTCTGCTGGAGAAGAGTCACGTGGACAGGGAACGCCTGGATGAAAAAGCTGGGAAAACCCCCTTGGAAACGCACAACA
AGGGTTGTTCCATTGCTGCCACAGGCAAAAGGCCATCTGCCCACTTCCCCACCAGCAGAGGAAGAAGAGGAGGGAGATGG
ACGATGGGCTCGCTGAGGGGGGTCCTCAGAGATCCAATACCTATGTGATCAAGCTATTTGACCGGAGTGTGGACTTGGCC
CAGTTCAGTGAGAACACACCACTGTACCCCATTTGCTTCGCCTGGATGCGCAACAGCTCCACAGTGTGAGAGCGCGAGCA
CTCATCCTGCTCACCACTGCCTCCTCTTCCAGAGGATGGAGAGGGTTCAGAGGTCATCAACAGCAAAAACCATGATGTGT
ACAAGCTGCCTCCACCCACAGTCCCTGGACCACTTGGAGATGCCTGTAGATCCAGAAATCCATCCCCACTGCAGCCTGAC
ACCCAGGGTACCCCTGATGAGGAACCTTCCGAGACTGAACCTTCTCCTTCCACACTTATCTATAGCAACATGCAACGTTG
GAAACGCATACGCCAGAGGTGGGAGGAGGCATTTCATTGGAACCAGCTTCGTTACTCAGAAAGTATGAAGATCCTACGGG
AGATGTATGACCGGCAG

Alignment

ORF - retro_mmus_2542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFPVKVKVEKSEMEMAKARNQLDAVLQCLLEKSHMDRERLDEEAGKTPLDTHNKDCSIAATGKRPSARFP
          MFPVKVKVEKSEMEMAKARNQLDAVLQCLLEKSH.DRERLDE.AGKTPL.THNK.CSIAATGKRPSA.FP
Retrocopy MFPVKVKVEKSEMEMAKARNQLDAVLQCLLEKSHVDRERLDEKAGKTPLETHNKGCSIAATGKRPSAHFP

Parental  -HQRRKKRREMDDGLAEGGPQRSNTYVIKLFDRSVDLAQFSENTPLYPICRAWMRNSPTVRERERSPGSP
          .HQ.RKKRREMDDGLAEGGPQRSNTYVIKLFDRSVDLAQFSENTPLYPIC.AWMRNS.TV.ERE.S..SP
Retrocopy <HQQRKKRREMDDGLAEGGPQRSNTYVIKLFDRSVDLAQFSENTPLYPICFAWMRNSSTV*EREHSSCSP

Parental  LPPLPEDGEGSEVINSKNRDVYKLPPPTAPGPLGDACRSRIPSPLQPETEGTPDDEPSEPEPSPSTLIYR
          LPPLPEDGEGSEVINSKN.DVYKLPPPT.PGPLGDACRSR.PSPLQP.T.GTPD.EPSE.EPSPSTLIY.
Retrocopy LPPLPEDGEGSEVINSKNHDVYKLPPPTVPGPLGDACRSRNPSPLQPDTQGTPDEEPSETEPSPSTLIYS

Parental  NMQRWKRIRQRWKEASHRNQLRYSESMKILREMYDRQ
          NMQRWKRIRQRW.EA.H.NQLRYSESMKILREMYDRQ
Retrocopy NMQRWKRIRQRWEEAFHWNQLRYSESMKILREMYDRQ

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	15.05 RPM
SRP007412_cerebellum	0.00 RPM	16.28 RPM
SRP007412_heart	0.00 RPM	6.44 RPM
SRP007412_kidney	0.02 RPM	6.49 RPM
SRP007412_liver	0.00 RPM	5.22 RPM
SRP007412_testis	0.00 RPM	10.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2542 was not detected

EST

No EST(s) were mapped for retro_mmus_2542 retrocopy.

TSS

No TSS is located nearby retro_mmus_2542 retrocopy 5' end.

Lab

retro_mmus_2542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2542 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010100	1 retrocopy	retro_cjac_2736,
Echinops telfairi	ENSETEG00000004801	1 retrocopy	retro_etel_199,
Mus musculus	ENSMUSG00000036845	1 retrocopy	retro_mmus_2542 ,
Tursiops truncatus	ENSTTRG00000003834	1 retrocopy	retro_ttru_1074,