RetrogeneDB ID: retro_mmus_2131

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:174046752..174047273(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082519
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vamp7
• Ensembl ID: ENSMUSG00000051412
• Aliases: Vamp7, Sybl1, TI-VAMP, VAMP-7
• Description: vesicle-associated membrane protein 7 [Source:MGI Symbol;Acc:MGI:1096399]

Sequence

>retro_mmus_2131
ATGGCCATTCTTTTTGCTGTTGTTGCCAGGGGAACCACTATCCTTGCCAAACATGCTTGGTGTGGAGGAAACTTCCTGGA
GGTGACAGAGCAGATTCTGGCTAAGACGCCTTCTGAAAATAATAAACTAACTTGCTCACATGGCAATTATTTGTGTCGTT
ACGTCTGCCAAGACAGGATCGCGTATCTTTGTATCACCGATGATGAGTTTGAGCGTTCTCGAGCCTTCAGTTTTTTGAAC
GAAGTAAAGAAGAGATTCCAGACAACTTACGGTTCTAGAGCAAGACTGCACTTCCTTATGCCGTGAATAGCGAGTTTTCA
AGCATTTTGGCTGCACCACTGAAGCACCGCTCCGAGAATAAGAGCCTAGACAAAGCAATGGAGACTCAAGCACAAGCGGA
TGAACTGAAAGGAGTAATGGTCAGAAACATAGATTTGGTTGCTCAACGTGGAGAAAGGTTGGAATTGCTGATAGATAAAA
CAGAAACCCTTGTGGATTCATCTGTCACTTTCAAAACTACC

Alignment

ORF - retro_mmus_2131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 79.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDF
          MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAK.PSENNKLT.SHGNYL..Y.CQDRI.YLCITDD.F
Retrocopy MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKTPSENNKLTCSHGNYLCRYVCQDRIAYLCITDDEF

Parental  ERSRAFSFLNEVKKRFQTTYGSRA-QTALPYAMNSEFSSVLAAQLKHHSENKSLDKVMETQAQVDELKGI
          ERSRAFSFLNEVKKRFQTTYGSRA..TALPYA.NSEFSS.LAA.LKH.SENKSLDK.METQAQ.DELKG.
Retrocopy ERSRAFSFLNEVKKRFQTTYGSRA<KTALPYAVNSEFSSILAAPLKHRSENKSLDKAMETQAQADELKGV

Parental  MVRNIDLVAQRGERLELLIDKTENLVDSSVTFKTT
          MVRNIDLVAQRGERLELLIDKTE.LVDSSVTFKTT
Retrocopy MVRNIDLVAQRGERLELLIDKTETLVDSSVTFKTT

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	18.39 RPM
SRP007412_cerebellum	0.00 RPM	13.50 RPM
SRP007412_heart	0.00 RPM	6.51 RPM
SRP007412_kidney	0.08 RPM	11.49 RPM
SRP007412_liver	0.05 RPM	18.32 RPM
SRP007412_testis	0.00 RPM	1.10 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2131 was not detected

EST

No EST(s) were mapped for retro_mmus_2131 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_84139	43 libraries	21 libraries	342 libraries	523 libraries	143 libraries

The graphical summary, for retro_mmus_2131 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2131 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016289	2 retrocopies	retro_cjac_1958, retro_cjac_2410,
Cavia porcellus	ENSCPOG00000024405	1 retrocopy	retro_cpor_714,
Mus musculus	ENSMUSG00000051412	1 retrocopy	retro_mmus_2131 ,
Oryctolagus cuniculus	ENSOCUG00000001270	1 retrocopy	retro_ocun_842,
Pteropus vampyrus	ENSPVAG00000000829	1 retrocopy	retro_pvam_513,
Ictidomys tridecemlineatus	ENSSTOG00000025036	1 retrocopy	retro_itri_720,
Tursiops truncatus	ENSTTRG00000010643	1 retrocopy	retro_ttru_66,