RetrogeneDB ID: retro_mmus_3251

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:19691063..19691548(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Bnip2
• Ensembl ID: ENSMUSG00000011958
• Aliases: None
• Description: BCL2/adenovirus E1B interacting protein 2 [Source:MGI Symbol;Acc:MGI:109327]

Sequence

>retro_mmus_3251
GTTGTTAGCCATGGAGGCTATGATGGGGATGGCTTAAATGCCATTGTTGTATTTGCTGTCTGTTTCATGCCTGAGAGTGG
TCAGCCTAATTATAGATATTTGATGGACAGTCTCTTTAATTATTGCATTGTCACTTTAGAGCTGTTGGTAGCAGAGACCT
ACATGATCATTTACTTAAATGGTGAGACAACTCAAAGAAAAATGCCCAGTCTGGGATGGCTCGGGAGATGCTACCAGCAA
ACTGATAGACGATTAAGGGAAAACCTAAAGTCTCTAATCATTATGCACCCTTCTTGGTTTATGCGAACACTTCTGGCTGT
TACAAGACCATTTATCAGTTCAAAATTCGGTCAGAAAATTATATACTTCTTTAAGTTAGCAGAACTGGTGGAGCTGTTCC
CAAGGAGTATGTTGGCATACCAGAGTGCATCAAATAATTTGATCAAGAGCTTAATAGAAAACAAGAACCACCAAAAAGTG
AGCAG

Alignment

ORF - retro_mmus_3251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 51.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VISHGGYYGDGLNAIVVFAVCFMPESGQPNYRYLMDNLFKYVIGTLELLVAENYMIIYLNGATTRRKMPS
          V.SHGGY.GDGLNAIVVFAVCFMPESGQPNYRYLMD.LF.Y.I.TLELLVAE.YMIIYLNG.TT.RKMPS
Retrocopy VVSHGGYDGDGLNAIVVFAVCFMPESGQPNYRYLMDSLFNYCIVTLELLVAETYMIIYLNGETTQRKMPS

Parental  LGWLRRCYQQIDRRLRKNLKSLIIVHPSWFIRTLLAVTRPFISSKFSQKIRYVFNLAELAEL-VPMEYVG
          LGWL.RCYQQ.DRRLR.NLKSLII.HPSWF.RTLLAVTRPFISSKF.QKI.Y.F.LAEL.EL.VP.EYVG
Retrocopy LGWLGRCYQQTDRRLRENLKSLIIMHPSWFMRTLLAVTRPFISSKFGQKIIYFFKLAELVEL<VPKEYVG

Parental  IPECIKQVDQELNGKQEPPKSEQ
          IPECIK..DQELN.KQEPPKSEQ
Retrocopy IPECIK*FDQELNRKQEPPKSEQ

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	0.02 RPM	25.56 RPM
SRP007412_cerebellum	0.00 RPM	34.82 RPM
SRP007412_heart	0.00 RPM	93.67 RPM
SRP007412_kidney	0.00 RPM	56.69 RPM
SRP007412_liver	0.03 RPM	58.96 RPM
SRP007412_testis	0.05 RPM	40.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3251 was not detected

EST

No EST(s) were mapped for retro_mmus_3251 retrocopy.

TSS

No TSS is located nearby retro_mmus_3251 retrocopy 5' end.

Lab

retro_mmus_3251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3251 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004962	2 retrocopies	retro_cpor_393, retro_cpor_935,
Mus musculus	ENSMUSG00000011958	1 retrocopy	retro_mmus_3251 ,