RetrogeneDB ID: retro_mmus_1851

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:10175856..10176161(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vamp3
• Ensembl ID: ENSMUSG00000028955
• Aliases: Vamp3, D130027G05Rik, VAMP-3, ceb
• Description: vesicle-associated membrane protein 3 [Source:MGI Symbol;Acc:MGI:1321389]

Sequence

>retro_mmus_1851
TCTACAGGTGTGCCTTGCGGGTCAAGTGCTGCCACTGGCAGTAATCAAAGACTCCAGCAGACACAAAATCAAGCAGGTGA
GGTGGTTGACATCACGAGAGTCCATGTGGATAAGGTGTTAGAACAGACCAGAAGCTCTCGGAGCTAGATGGCCGGGCAGA
TGCACTGCTGGCAGGTGCCTCGCAGTTTGAAACAAGTGCTGCCAAGTTGAAGAGAAAGTATTGGTGGAAGAACTACAAGA
TGTGGGTGATAGGGATCAGTGTCCTGGTGATTATTGTCACCATCATCATCGTGCGGTGTGTCTCT

Alignment

ORF - retro_mmus_1851 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.41 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STGVPSGSSAATGSNRRLQQTQNQVDEVVDIMRVNVDKVLER-DQKLSELDDRADALQAGASQFETSAAK
          STGVP.GSSAATGSN.RLQQTQNQ..EVVDI.RV.VDKVLE..DQKLSELD.RADAL.AGASQFETSAAK
Retrocopy STGVPCGSSAATGSNQRLQQTQNQAGEVVDITRVHVDKVLEQ<DQKLSELDGRADALLAGASQFETSAAK

Parental  LKRKYWWKNCKMWAIGISVLVIIVIIIIVWCVS
          LKRKYWWKN.KMW.IGISVLVIIV.IIIV.CVS
Retrocopy LKRKYWWKNYKMWVIGISVLVIIVTIIIVRCVS

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	26.05 RPM
SRP007412_cerebellum	0.00 RPM	25.84 RPM
SRP007412_heart	0.00 RPM	40.38 RPM
SRP007412_kidney	0.02 RPM	39.62 RPM
SRP007412_liver	0.00 RPM	15.68 RPM
SRP007412_testis	0.00 RPM	44.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1851 was not detected

EST

No EST(s) were mapped for retro_mmus_1851 retrocopy.

TSS

No TSS is located nearby retro_mmus_1851 retrocopy 5' end.

Lab

retro_mmus_1851 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1851 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005770	1 retrocopy	retro_mdom_273,
Mus musculus	ENSMUSG00000028955	1 retrocopy	retro_mmus_1851 ,
Otolemur garnettii	ENSOGAG00000009797	1 retrocopy	retro_ogar_2300,
Procavia capensis	ENSPCAG00000004825	1 retrocopy	retro_pcap_389,
Tarsius syrichta	ENSTSYG00000007733	6 retrocopies	retro_tsyr_1027, retro_tsyr_1435, retro_tsyr_1634, retro_tsyr_1757, retro_tsyr_524, retro_tsyr_968,