RetrogeneDB ID: retro_mmus_827

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:99839975..99840260(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082531
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sumo2
• Ensembl ID: ENSMUSG00000020738
• Aliases: Sumo2, SUMO-2, Smt3A, Smt3b, Smt3h2
• Description: SMT3 suppressor of mif two 3 homolog 2 (yeast) [Source:MGI Symbol;Acc:MGI:2158813]

Sequence

>retro_mmus_827
ATTGCTGATGAGAAACCCAAGGATGGCGTCAAGACTGAGAACAACGATCATATTAACTTGAAGGTAGCAGGACAGGATGG
TTTTGTGGTGCAGTGTAAGATTAAGAGACGTACATCACTCAGTAAACTAATGAAAGCCTATTGTGAATGGCAGGGTTTGT
CAAAGAGGCAGATCAGATTCTGGTTTGATGGGCAACCTATCAATGAAACAGACTCACTTGGCCAGTGGGAAATAGAGGAT
GAAGATATGATTGATGTGTTCCAGCAGCAGACTGGAGGTGTCTAC

Alignment

ORF - retro_mmus_827 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINET
          .ADEKPK.GVKTENNDHINLKVAGQDG.VVQ.KIKR.T.LSKLMKAYCE.QGLS.RQIRF.FDGQPINET
Retrocopy IADEKPKDGVKTENNDHINLKVAGQDGFVVQCKIKRRTSLSKLMKAYCEWQGLSKRQIRFWFDGQPINET

Parental  DTPAQLEMEDEDTIDVFQQQTGGVY
          D...Q.E.EDED.IDVFQQQTGGVY
Retrocopy DSLGQWEIEDEDMIDVFQQQTGGVY

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	1.00 RPM
SRP007412_cerebellum	0.00 RPM	0.78 RPM
SRP007412_heart	0.03 RPM	0.72 RPM
SRP007412_kidney	0.00 RPM	0.87 RPM
SRP007412_liver	0.00 RPM	0.25 RPM
SRP007412_testis	0.00 RPM	1.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_827 was not detected

EST

No EST(s) were mapped for retro_mmus_827 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_20228	846 libraries	204 libraries	15 libraries	5 libraries	2 libraries

The graphical summary, for retro_mmus_827 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_827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_827 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004724	1 retrocopy	retro_cfam_484,
Homo sapiens	ENSG00000188612	2 retrocopies	retro_hsap_4036, retro_hsap_4095,
Gorilla gorilla	ENSGGOG00000023769	3 retrocopies	retro_ggor_101, retro_ggor_184, retro_ggor_2576,
Loxodonta africana	ENSLAFG00000025811	10 retrocopies	retro_lafr_104, retro_lafr_1222, retro_lafr_1240, retro_lafr_200, retro_lafr_254, retro_lafr_324, retro_lafr_36, retro_lafr_488, retro_lafr_858, retro_lafr_888,
Monodelphis domestica	ENSMODG00000007222	11 retrocopies	retro_mdom_1263, retro_mdom_1472, retro_mdom_1474, retro_mdom_1560, retro_mdom_1598, retro_mdom_1755, retro_mdom_237, retro_mdom_378, retro_mdom_517, retro_mdom_788, retro_mdom_986,
Mus musculus	ENSMUSG00000020265	1 retrocopy	retro_mmus_3548,
Mus musculus	ENSMUSG00000020738	19 retrocopies	retro_mmus_1498, retro_mmus_1772, retro_mmus_1903, retro_mmus_2050, retro_mmus_2323, retro_mmus_2475, retro_mmus_2492, retro_mmus_2590, retro_mmus_2767, retro_mmus_2917, retro_mmus_2974, retro_mmus_3209, retro_mmus_3414, retro_mmus_3630, retro_mmus_415, retro_mmus_611, retro_mmus_689, retro_mmus_818, retro_mmus_827 ,
Mus musculus	ENSMUSG00000026021	5 retrocopies	retro_mmus_1594, retro_mmus_2129, retro_mmus_2135, retro_mmus_252, retro_mmus_2962,
Oryctolagus cuniculus	ENSOCUG00000028195	5 retrocopies	retro_ocun_110, retro_ocun_136, retro_ocun_175, retro_ocun_22, retro_ocun_46,
Pongo abelii	ENSPPYG00000029777	2 retrocopies	retro_pabe_164, retro_pabe_84,