RetrogeneDB ID: retro_mmus_1257

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:22775017..22775421(-)
• Located in intron of: ENSMUSG00000063458

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snapin
• Ensembl ID: ENSMUSG00000001018
• Aliases: Snapin, 25kDa, AA407989, AV026596, Bloc1s7, Snap25bp, Snapap
• Description: SNAP-associated protein [Source:MGI Symbol;Acc:MGI:1333745]

Sequence

>retro_mmus_1257
ATGGCCGCAGCTGGTTTCGCTGTGTCAGGGGCCAGAACCCCAGTGGTGGGGCCCACAGGCCGTGACCTCTTTGCTGAGGG
CCTCCTGGAGTTCCTGCGACCTGCTATGCAGCAGCTCGACTCTCACATACACGAGGTCAGAGAAAGCCAAGTAAAGCTCC
GGGAACAAAATGACAACCTAGCTACAGAACTATGCCAGATCAATGAGGATCAGAAGGTCGCCCTGGATCTGGACCGCTAT
GTTAAGAAGGTGCTAATGCCAGGCAACGAGATGTCTTTGTCAACAATATTTTACATAATGCACAGGAACGTCTAAGGCAG
CAAAACCACAGTGTGGCCAAGGAAACAGCTCGAAGGAGAGCCATGCTGGATTCAGGAGTTTACCCTCCTGGTTCTCCAAG
CAAA

Alignment

ORF - retro_mmus_1257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAGSAAVSGAGTPVAGPTGRDLFAEGLLEFLRPAVQQLDSHVHAVRESQVELREQIDNLATELCRINE
          MAAAG.A.VSGA.TPV.GPTGRDLFAEGLLEFLRPA.QQLDSH.H.VRESQV.LREQ.DNLATELC.INE
Retrocopy MAAAGFA-VSGARTPVVGPTGRDLFAEGLLEFLRPAMQQLDSHIHEVRESQVKLREQNDNLATELCQINE

Parental  DQKVALDLDPYVKKLL-NARRRVVLVNNILQNAQERLRRLNHSVAKETARRRAMLDSGVYPPGSPSK
          DQKVALDLD.YVKK.L.NAR.R.V.VNNIL.NAQERLR..NHSVAKETARRRAMLDSGVYPPGSPSK
Retrocopy DQKVALDLDRYVKKVL<NARQRDVFVNNILHNAQERLRQQNHSVAKETARRRAMLDSGVYPPGSPSK

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	27.40 RPM
SRP007412_cerebellum	0.00 RPM	24.71 RPM
SRP007412_heart	0.03 RPM	42.59 RPM
SRP007412_kidney	0.08 RPM	19.90 RPM
SRP007412_liver	0.00 RPM	7.65 RPM
SRP007412_testis	0.00 RPM	32.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1257 was not detected

EST

No EST(s) were mapped for retro_mmus_1257 retrocopy.

TSS

No TSS is located nearby retro_mmus_1257 retrocopy 5' end.

Lab

retro_mmus_1257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1257 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003301	1 retrocopy	retro_chof_723,
Callithrix jacchus	ENSCJAG00000010373	1 retrocopy	retro_cjac_742,
Dasypus novemcinctus	ENSDNOG00000015216	1 retrocopy	retro_dnov_1023,
Mus musculus	ENSMUSG00000001018	1 retrocopy	retro_mmus_1257 ,
Sorex araneus	ENSSARG00000013451	1 retrocopy	retro_sara_19,