RetrogeneDB ID: retro_mmus_252

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:51756742..51757096(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000062224
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Sumo1
• Ensembl ID: ENSMUSG00000026021
• Aliases: Sumo1, GMP1, PIC1, SENTRIN, SMT3, SMT3H3, SMTP3, SUMO-1, Smt3C, Ubl1
• Description: SMT3 suppressor of mif two 3 homolog 1 (yeast) [Source:MGI Symbol;Acc:MGI:1197010]

Sequence

>retro_mmus_252
ATGTTTGACCAGGAGGCTAAACCTTCAAGTGGTGTCTTAGAGGATGAGAAGAAAGATGTTATTAAAGTCAAAGTTATTGG
AGAAGATAGAAGTGAGATACACTTCAGACTGAAAATGACAACAAGGCTCAAGAAACTTAAGGACTCATACAGTCGAAGAC
TGGATCTGTCAGTGAATTCACTGAGGTTTCTCTTTGAAGGCCAGAAGATTGCCGATGACCATACTGCAGAAGAGCTGGGG
ATGGAGGAGGAAGACGTGATTGAAGTCCATCAGGAACAAACGGGAGGTGGAGTGTCACTCGACAGCTTAGGAAGATCTGA
CAGAAATCTATCTGGAAAAATAGGAAATCATTAA

Alignment

ORF - retro_mmus_252 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.1 %
• Parental protein coverage: 96.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQR
          M.DQEAKPS...L.D.K....IK.KVIG.D.SEIHF..KMTT.LKKLK.SY..R.....NSLRFLFEGQ.
Retrocopy MFDQEAKPSSGVLEDEKK-DVIKVKVIGEDRSEIHFRLKMTTRLKKLKDSYSRRLDLSVNSLRFLFEGQK

Parental  IADNHTPKELGMEEEDVIEVYQEQTGG
          IAD.HT..ELGMEEEDVIEV.QEQTGG
Retrocopy IADDHTAEELGMEEEDVIEVHQEQTGG

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	24.86 RPM
SRP007412_cerebellum	0.00 RPM	23.27 RPM
SRP007412_heart	0.00 RPM	14.60 RPM
SRP007412_kidney	0.00 RPM	20.67 RPM
SRP007412_liver	0.03 RPM	12.70 RPM
SRP007412_testis	7.00 RPM	24.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_252 was not detected

EST

No EST(s) were mapped for retro_mmus_252 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_3707	1066 libraries	2 libraries	2 libraries	0 libraries	2 libraries
TSS #2	TSS_3708	1066 libraries	2 libraries	2 libraries	0 libraries	2 libraries

The graphical summary, for retro_mmus_252 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_252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_252 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Choloepus hoffmanni	ENSCHOG00000009739	2 retrocopies	retro_chof_190, retro_chof_2068,
Callithrix jacchus	ENSCJAG00000004961	3 retrocopies	retro_cjac_1686, retro_cjac_1932, retro_cjac_2610,
Cavia porcellus	ENSCPOG00000012143	1 retrocopy	retro_cpor_1279,
Equus caballus	ENSECAG00000024693	4 retrocopies	retro_ecab_199, retro_ecab_365, retro_ecab_570, retro_ecab_935,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Homo sapiens	ENSG00000116030	5 retrocopies	retro_hsap_2007, retro_hsap_240, retro_hsap_2489, retro_hsap_262, retro_hsap_897,
Gorilla gorilla	ENSGGOG00000026439	5 retrocopies	retro_ggor_1451, retro_ggor_1550, retro_ggor_299, retro_ggor_311, retro_ggor_725,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Mustela putorius furo	ENSMPUG00000000335	2 retrocopies	retro_mputfur_257, retro_mputfur_33,
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,
Nomascus leucogenys	ENSNLEG00000006997	4 retrocopies	retro_nleu_277, retro_nleu_384, retro_nleu_855, retro_nleu_865,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Rattus norvegicus	ENSRNOG00000016133	2 retrocopies	retro_rnor_2015, retro_rnor_813,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,
Ictidomys tridecemlineatus	ENSSTOG00000025405	4 retrocopies	retro_itri_1193, retro_itri_1232, retro_itri_216, retro_itri_668,
Tursiops truncatus	ENSTTRG00000000642	4 retrocopies	retro_ttru_1646, retro_ttru_1652, retro_ttru_309, retro_ttru_399,