RetrogeneDB ID: retro_mmus_580

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:82585425..82586680(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094683
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ap3m1
• Ensembl ID: ENSMUSG00000021824
• Aliases: None
• Description: adaptor-related protein complex 3, mu 1 subunit [Source:MGI Symbol;Acc:MGI:1929212]

Sequence

>retro_mmus_580
ATGATCCACAGTCTATTTCTCATAAACTGCTCTGGCGACATTTTTCTAGAAAAACACTGGAAGAGCGTTGTAAGCCAGTC
AGTGTGTGACTATTTCTTTGAAGCTCAGGAGAAAGCTGCTGATGTTGAAAATGTCCCACCTATCATTTCAACACCTCACC
ACTACCTCATTAGTATCTACCGGGATAAGCTCTTCTTTGTGTCTGTGATACAGACCGAAGTGCCACCTCTCTTTGTAATT
GAATTTCTGCATCGAGTTGCTGACACTTTTCAGGACTACTTTGGTGAGTGTTCAGAGGCTGCAATTAAGGATAATGTGGT
CATAGTATATGAGCTCTTGGAAGAAATGTTAGACAATGGATTCCCACTGACTACTGAATCTAACATTTTGAAAGAACTGA
TTAAACCACCAACAATTCTACGTTCTGTCGTCAATTCTATTACAGGCAGTAGTAATGTTGGGGATACACTCCCCACTGGG
CAGCTATCCAACATCCCATGGCGTCGAGCAGGAGTAAAGTACACAAACAATGAAGCCTATTTTGATGTAGTTGAAGAGAT
AGATGCAATTATAGATAAATCAGGATCTACAGTCTTTGCAGAAATTCAAGGGGTCATTGATGCTTGCATTAAGCTGTCTG
GAATGCCTGATCTCTCCCTCTCTTTCATGAACCCAAGGCTCCTAGATGACGTCAGCTTCCACCCATGCATCCGATTCAAA
CGCTGGGAGTCTGAAAGAGTTTTGTCATTCATTCCTCCAGATGGAAATTTCCGACTCATATCGTATCGTGTCAGCTCACA
AAATCTAGTGGCAATACCAGTGTATGTGAAACACAGTATCAGCTTTAAGGAAAACAGCTCTTGTGGCCGGTTTGATATAA
CAATTGGACCGAAACAGAATATGGGAAAAACAATTGAAGGAATCACAGTGACTGTTCACATGCCCAAAGTTGTGCTGAAT
ATGAACCTGACACCAACGCAAGGCAGCTATACATTTGATCCAGTGACCAAGGTACTAGCATGGGATGTGGGCAAAATTAC
TCCACAAAAGCTCCCAAGTCTTAAAGGACTAGTAAATTTACAGTCAGGAGCACCCAAGCCAGAAGAGAACCCAAACCTCA
ACATACAGTTCAAGATCCAGCAGCTTGCTATTTCAGGCTTAAAAGTGAACCCGCTTGGACATGTATGGTGAGAAGTATAA
GCCATTTAAAGAAGTCAAATATGTCACAAAGGCTGGGAAGTTCCAAGTGAGGACA

Alignment

ORF - retro_mmus_580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYRDKLFFVSVI
          MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPP.ISTPHHYLISIYRDKLFFVSVI
Retrocopy MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPIISTPHHYLISIYRDKLFFVSVI

Parental  QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTIL
          QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPL.TESNILKELIKPPTIL
Retrocopy QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLTTESNILKELIKPPTIL

Parental  RSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACI
          RSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACI
Retrocopy RSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACI

Parental  KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI
          KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI
Retrocopy KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI

Parental  SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLAWDVGKITPQK
          SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLAWDVGKITPQK
Retrocopy SFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLAWDVGKITPQK

Parental  LPSLKGLVNLQSGAPKPEENPNLNIQFKIQQLAISGLKVN-RLDMYGEKYKPFKGVKYVTKAGKFQVRT
          LPSLKGLVNLQSGAPKPEENPNLNIQFKIQQLAISGLKVN.RLDMYGEKYKPFK.VKYVTKAGKFQVRT
Retrocopy LPSLKGLVNLQSGAPKPEENPNLNIQFKIQQLAISGLKVN>RLDMYGEKYKPFKEVKYVTKAGKFQVRT

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	0.07 RPM	32.80 RPM
SRP007412_cerebellum	0.04 RPM	29.01 RPM
SRP007412_heart	0.03 RPM	16.81 RPM
SRP007412_kidney	0.06 RPM	22.56 RPM
SRP007412_liver	0.22 RPM	99.29 RPM
SRP007412_testis	0.18 RPM	14.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_580 was not detected

EST

No EST(s) were mapped for retro_mmus_580 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_6508	108 libraries	102 libraries	748 libraries	102 libraries	12 libraries

The graphical summary, for retro_mmus_580 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_580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_580 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004510	1 retrocopy	retro_chof_2586,
Monodelphis domestica	ENSMODG00000000660	1 retrocopy	retro_mdom_1564,
Mus musculus	ENSMUSG00000021824	1 retrocopy	retro_mmus_580 ,
Mus musculus	ENSMUSG00000022841	2 retrocopies	retro_mmus_1873, retro_mmus_1914,
Ictidomys tridecemlineatus	ENSSTOG00000012881	1 retrocopy	retro_itri_1276,