RetrogeneDB ID: retro_mmus_1250

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:18543807..18545132(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vps4b
• Ensembl ID: ENSMUSG00000009907
• Aliases: None
• Description: vacuolar protein sorting 4b (yeast) [Source:MGI Symbol;Acc:MGI:1100499]

Sequence

>retro_mmus_1250
ATGGCGTCCACGAACACCAACCTCCAGAAAGCAATAGATCTTGCAAGCAAAGCAGCCCAGGAAGACAAAGCTGGGAACTA
TGAGGAAGCTCTTCAACTCTACCAACATGCTGTGCAGTATTTTCTCCATGTTGTTAAATATGAAGCACAAGGTGATAAAG
CCAAGCAAAGTATCGGGACCAAGTGTACAGAATATCTTGATAGAGCAGAAAAACTAAAGGAATATCTGAAGAAAAGAGAG
AAGAAACCACAGAAGCCCGTGAAAGAGGAACAGTCAGGCCCAGATGATGAAAAGGGGAATGACAGTGATGGGGATGCAGA
ATCTGATGATCCTGAAAAAAAGAAACTGCAGAATCAACTTCAAGGTGCCATTGTTATAGAGCGACCAAATGTGAAATGGA
GTGATGTTGCTGGTCTCGAAGGAGCCAAAGAAGCTCTTAAAGAGTCTGTGATTCTGCTTATTAAGTTCCCTCATCTGTTT
ACAGGGAAGAGGACACCTTGGAGAGGAATCCTATTATTTGGACCACCAGGAACAGGAAAATCTTATTTGCCTAAAGCTGT
TGCAACGGAAGCAAACAACTCAACATCTTTCTCAATATCTTCCTCTGACCTTGTGTCTAAGTGGCTGGGGGAAAGGGAAA
AACTGGTTAAGAACTTATTACAGGTTGCCAGAGAGAACAAGCCTTCTATCATCTTCATTGATGAGATTGATTCTCTGTGT
GGTTCCAGAAGTGAGAATGAGAGTGAAGCTGCACAGAGAATTAAGACAGAGTTCCTGGTTCAAATGCAAGGAGTTGGTGT
GGACAATGATGGAATTTTGGTTCTGGGAGCTACAAATATACCCTGGGTTCTGGATTCTGCAATTAGGCGAAGATTTGAGA
AACATATTTATATTCCTTTGCCCGAAGCCCATGCCCGAGCAGCCATGTTTAGACTGCACTTGGGCATCACTCAGAACAGC
CTCACAGAAGCAGAATTCCAAGAACTTGGAAGGAAGACAGATGGCTATTCAGGAGCAGATATAAGTATCATTGTATGGGA
TGCACTTATGCAGCCTGTGAAAAAAGTCAGTCAGCTGCTCACTTCAAAAATGTTCGTGGACCCTCAAGAGCTGATCCTAA
CTGCATTGTAAATGACCTGCTGATCTCCTCTCCAGGAGATCCTGGGGCTATTGAAATGACATGGATGGATGTTCCTGGAG
ATACACTCTTGGAGCCAGTTGTTTCCATATGGGATATGCTGCGGTCCCTGTCCAACACAAAGCTGACAGTCAACGAGCAG
GACTTCTTGAAGCTGAAGAAGTTTACAGAAGATTTTTGCCAGGAA

Alignment

ORF - retro_mmus_1250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASTNTNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSIRAKCTEYLDRAE
          MASTNTNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSI..KCTEYLDRAE
Retrocopy MASTNTNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSIGTKCTEYLDRAE

Parental  KLKEYLKKKEKKPQKPVKEEQSGPVDEKGNDSDGEAESDDPEKKKLQNQLQGAIVIERPNVKWSDVAGLE
          KLKEYLKK.EKKPQKPVKEEQSGP.DEKGNDSDG.AESDDPEKKKLQNQLQGAIVIERPNVKWSDVAGLE
Retrocopy KLKEYLKKREKKPQKPVKEEQSGPDDEKGNDSDGDAESDDPEKKKLQNQLQGAIVIERPNVKWSDVAGLE

Parental  GAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLG
          GAKEALKE.VIL.IKFPHLFTGKRTPWRGILLFGPPGTGKSYL.KAVATEANNST.FSISSSDLVSKWLG
Retrocopy GAKEALKESVILLIKFPHLFTGKRTPWRGILLFGPPGTGKSYLPKAVATEANNSTSFSISSSDLVSKWLG

Parental  ESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNI
          E.EKLVKNL.Q.ARENKPSIIFIDEIDSLCGSRSENESEAA.RIKTEFLVQMQGVGVDNDGILVLGATNI
Retrocopy EREKLVKNLLQVARENKPSIIFIDEIDSLCGSRSENESEAAQRIKTEFLVQMQGVGVDNDGILVLGATNI

Parental  PWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALM
          PWVLDSAIRRRFEK.IYIPLPEAHARAAMFRLHLG.TQNSLTEA.FQELGRKTDGYSGADISIIV.DALM
Retrocopy PWVLDSAIRRRFEKHIYIPLPEAHARAAMFRLHLGITQNSLTEAEFQELGRKTDGYSGADISIIVWDALM

Parental  QPVRKV-QSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLS
          QPV.KV.QSA.HFK.VRGPSRADPNCIVNDLL...SPGDPGAIEMTWMDVPGD.LLEPVVS.WDMLRSLS
Retrocopy QPVKKV<QSAAHFKNVRGPSRADPNCIVNDLLI-SSPGDPGAIEMTWMDVPGDTLLEPVVSIWDMLRSLS

Parental  STKPTVNEQDLLKLKKFTEDFGQE
          .TK.TVNEQD.LKLKKFTEDF.QE
Retrocopy NTKLTVNEQDFLKLKKFTEDFCQE

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	0.12 RPM	45.09 RPM
SRP007412_cerebellum	0.00 RPM	35.82 RPM
SRP007412_heart	0.06 RPM	25.65 RPM
SRP007412_kidney	0.08 RPM	57.33 RPM
SRP007412_liver	0.11 RPM	55.38 RPM
SRP007412_testis	0.23 RPM	23.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1250 was not detected

EST

No EST(s) were mapped for retro_mmus_1250 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_33072	581 libraries	268 libraries	218 libraries	4 libraries	1 library

The graphical summary, for retro_mmus_1250 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_1250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1250 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000016525	1 retrocopy	retro_mputfur_1219,
Mus musculus	ENSMUSG00000009907	1 retrocopy	retro_mmus_1250 ,
Mus musculus	ENSMUSG00000031913	1 retrocopy	retro_mmus_1038,