RetrogeneDB ID: retro_mmus_3641

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:75475234..75475523(-)
• Located in intron of: ENSMUSG00000083093

Retrocopy information

• Ensembl ID: ENSMUSG00000048709
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hmgn1
• Ensembl ID: ENSMUSG00000040681
• Aliases: None
• Description: high mobility group nucleosomal binding domain 1 [Source:MGI Symbol;Acc:MGI:96120]

Sequence

>retro_mmus_3641
ATGCCCAAGAGGAAGGTTAGCGCGGATGGAGCGGCCAAGGCGGAGCCCAAGTGCCTCTCCGCGAGGCTGTCGGCCAAGCC
CGCCCCTGCCAAGGTGGACGCGAAGCCGGAAAAAGGCCGCGGGAAAGGATAAAGCATCAGACAAAAAAGTGCAGATAAAA
GGGAAGAGGGGAGCGAAGAGCAAACAGGCTGACGTGGCTGACCAGGAAACCACAGAGCTGCCTGCAGAAAATGGAGAGAC
GGAAAACCAGAGTCCAGCCTCTGAAGAAGAGAAAGAAGCTAAGTCCGAC

Alignment

ORF - retro_mmus_3641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKVSADGAAKAEPKRRSARLSAKPAPAKVDAKP-KKAAGKDKASDKKVQIKGKRGAKGKQADVADQQ
          MPKRKVSADGAAKAEPK..SARLSAKPAPAKVDAKP.KKAAGKDKASDKKVQIKGKRGAK.KQADVADQ.
Retrocopy MPKRKVSADGAAKAEPKCLSARLSAKPAPAKVDAKP>KKAAGKDKASDKKVQIKGKRGAKSKQADVADQE

Parental  TTELPAENGETENQSPASEEEKEAKSD
          TTELPAENGETENQSPASEEEKEAKSD
Retrocopy TTELPAENGETENQSPASEEEKEAKSD

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	0.02 RPM	27.59 RPM
SRP007412_cerebellum	0.04 RPM	26.14 RPM
SRP007412_heart	0.03 RPM	21.23 RPM
SRP007412_kidney	0.04 RPM	50.01 RPM
SRP007412_liver	0.08 RPM	36.43 RPM
SRP007412_testis	0.09 RPM	25.52 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_3641 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	X:75475280..75475808

EST

No EST(s) were mapped for retro_mmus_3641 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_158030	347 libraries	477 libraries	242 libraries	5 libraries	1 library

The graphical summary, for retro_mmus_3641 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_3641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3641 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002336	7 retrocopies	retro_cpor_1129, retro_cpor_1389, retro_cpor_334, retro_cpor_349, retro_cpor_4, retro_cpor_884, retro_cpor_949,
Monodelphis domestica	ENSMODG00000020972	5 retrocopies	retro_mdom_1085, retro_mdom_109, retro_mdom_284, retro_mdom_755, retro_mdom_88,
Mus musculus	ENSMUSG00000040681	13 retrocopies	retro_mmus_1274, retro_mmus_1295, retro_mmus_1445, retro_mmus_1565, retro_mmus_1574, retro_mmus_1636, retro_mmus_2166, retro_mmus_2195, retro_mmus_2895, retro_mmus_3117, retro_mmus_3641 , retro_mmus_832, retro_mmus_949,
Rattus norvegicus	ENSRNOG00000048226	8 retrocopies	retro_rnor_1020, retro_rnor_1239, retro_rnor_1290, retro_rnor_2643, retro_rnor_2667, retro_rnor_642, retro_rnor_764, retro_rnor_966,
Rattus norvegicus	ENSRNOG00000050978	5 retrocopies	retro_rnor_1057, retro_rnor_1318, retro_rnor_1389, retro_rnor_2433, retro_rnor_358,