RetrogeneDB ID: retro_mmus_2986

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:6533930..6534511(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: 4930453N24Rik
• Ensembl ID: ENSMUSG00000059920
• Aliases: 4930453N24Rik, AI649104
• Description: RIKEN cDNA 4930453N24 gene [Source:MGI Symbol;Acc:MGI:1914859]

Sequence

>retro_mmus_2986
ATGTCGGAGCTTAGCCACTTAGAGTCAGAGGGATGCCGAAACCTATTTGGCATGCTGGACAATGATGAGATCATGGCCCT
TTGGGACACCATCACCACCACCTAGTGCAGCCTGTGGACCTCCAAGATGCTATTTGTGCAATATTAGTGTGTAGCCAACA
TGTAGAAGAACTTCTGAGGCTCAAAAAAGTCCACTGAGAAGTCATATTTAAGTATTTGGTAACACAAGGGGTGGTTGTAC
CTCCAACTACTGAAAATCACAATCTTATTCAGTATGTACAAGGTTACTCAGAAGAAGAGTCACCAAATCCAAAGGAGGCA
GCAGAGCCAGTTACAGAGACAGAGGACATCCAGCTCTTTGAACAGCAGACAAAAGAAGAGAAAGAAGCGGAAAAGGTTGA
TTATCATCACTTAGGAGAATTCTGTCACTGGTTCTTTGAAGTTCTTAATTCTCAGAATCCTTTTCTGGGACCACCTCAAG
ATGAATGTGGCCTACAGCACTTCTGGCATGATGTCCAGCTTAGGTTTTATTATAACACATCAGAACAAAGCATGACAGAC
TACCACAGAGCAGAAATTGTC

Alignment

ORF - retro_mmus_2986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.02 %
• Parental protein coverage: 56.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGLSHLESEGCRNLLGLLDNDEIMALCDTVT-NRLVQPVDRQDAIHAILVYSQNVEELLRRKKVHREVI
          MS.LSHLESEGCRNL.G.LDNDEIMAL.DT.T...LVQPVD.QDAI.AILV.SQ.VEELLR.KKVH.EVI
Retrocopy MSELSHLESEGCRNLFGMLDNDEIMALWDTIT<HHLVQPVDLQDAICAILVCSQHVEELLRLKKVH*EVI

Parental  FKYLAKQGVVVPPTAEKHNLIQYAKDYWAKQSPKLKDTAEPVTKTEDIQLFKQQAKEDKEAEKVDFRRLG
          FKYL..QGVVVPPT.E.HNLIQY...Y....SP..K..AEPVT.TEDIQLF.QQ.KE.KEAEKVD...LG
Retrocopy FKYLVTQGVVVPPTTENHNLIQYVQGYSEEESPNPKEAAEPVTETEDIQLFEQQTKEEKEAEKVDYHHLG

Parental  EEFCHWFFELLNSQNPFLGPPQDDWGPQHFWHDAKLRFYYNTSEQNTTDYQGAEIV
          .EFCHWFFE.LNSQNPFLGPPQD..G.QHFWHD..LRFYYNTSEQ..TDY..AEIV
Retrocopy -EFCHWFFEVLNSQNPFLGPPQDECGLQHFWHDVQLRFYYNTSEQSMTDYHRAEIV

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	16.38 RPM
SRP007412_cerebellum	0.00 RPM	18.11 RPM
SRP007412_heart	0.00 RPM	14.54 RPM
SRP007412_kidney	0.00 RPM	18.17 RPM
SRP007412_liver	0.00 RPM	15.70 RPM
SRP007412_testis	0.00 RPM	354.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2986 was not detected

EST

No EST(s) were mapped for retro_mmus_2986 retrocopy.

TSS

No TSS is located nearby retro_mmus_2986 retrocopy 5' end.

Lab

retro_mmus_2986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2986 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000059920	3 retrocopies	retro_mmus_2986 , retro_mmus_376, retro_mmus_695,
Tursiops truncatus	ENSTTRG00000002941	1 retrocopy	retro_ttru_1424,