RetrogeneDB ID: retro_mmus_597

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:106949303..106949869(+)
• Located in intron of: ENSMUSG00000035948

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sult1c2
• Ensembl ID: ENSMUSG00000023122
• Aliases: None
• Description: sulfotransferase family, cytosolic, 1C, member 2 [Source:MGI Symbol;Acc:MGI:1916333]

Sequence

>retro_mmus_597
CCCCTGCAGGCTGCATCTGTGGACAACTGAAGGCAGATTCAGACTTTCAATGCCAAGCCAGATGACCTCCTCATTTGTAT
TTATGCTAAATTCAGAATAACGTGGATTCAAGAAGTCATAGACATTATTTAACAGAATGGGAATGTAGAGATGTGCCAGT
GAGCTGTCATCTAACACCAGCACCCTTTATTAAGTGGGTGTGGCCACCCGACACATCAGGTGTGGACGAAGCCAATGAGA
TGCCAGTTCTGAGGATCCATCTTCCTGCTCAGCTGCTTGCCACCATCTTTCTGGAAAATAACTCTATGTTCTTTTATGTG
GCTTGGAACACCAATGAATGCATGGTTTCCTACTACCACTTGTGTAGGATGAGCCAGGTTCTCAGAGATCCAGGAACCTG
GGATGAGTATTTGGACACCTTCATCAATGGAAAAGTAAGTTGGGGATCTTGTATTGACCAGGAGGAATGCTGGAAAATTC
AACACAAACAACAGATTCTCTTCCTCTTCTCTGAAGCTATGATTATGGACTCAAACCATGAAATCCAGAAGGTAACGCAG
ATTTTG

Alignment

ORF - retro_mmus_597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.78 %
• Parental protein coverage: 65.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PLQAPTVDNWRQIQTFEAKPDDLLICTYPKSGTTWIQEIVDMIEQNGDVEKCRRTIIQHRHP-FIEWARP
          PLQA..VDN.RQIQTF.AKPDDLLIC.Y.K...TWIQE..D.I.QNG.VE.C....I.H.HP.FI.W..P
Retrocopy PLQAASVDN*RQIQTFNAKPDDLLICIYAKFRITWIQEVIDII*QNGNVEMCQ*AVI*HQHP<FIKWVWP

Parental  PQPSGVDKANEMPAPRILRTHLPTQLL-PPSFWT-NNCKFLYVARNAKDCMVSYYHFYRMSQVLPEPGTW
          P..SGVD.ANEMP....LR.HLP.QLL.PPSFW..NN..F.YVA.N...CMVSYYH..RMSQVL..PGTW
Retrocopy PDTSGVDEANEMP---VLRIHLPAQLL>PPSFWK<NNSMFFYVAWNTNECMVSYYHLCRMSQVLRDPGTW

Parental  DEYFETFINGKVSWGSWFDHVKGWWEIRDKYQILFLFYEDMKRNPKHEIQKVMQFM
          DEY..TFINGKVSWGS..D.....W.I..K.QILFLF.E.M.....HEIQKV.Q..
Retrocopy DEYLDTFINGKVSWGSCIDQ-EECWKIQHKQQILFLFSEAMIMDSNHEIQKVTQIL

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	0.19 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.06 RPM	68.78 RPM
SRP007412_liver	0.03 RPM	5.27 RPM
SRP007412_testis	0.00 RPM	0.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_597 was not detected

EST

No EST(s) were mapped for retro_mmus_597 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_135	1043 libraries	24 libraries	4 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_597 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_597 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_597 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2456

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000023122	1 retrocopy	retro_mmus_597 ,
Rattus norvegicus	ENSRNOG00000040215	1 retrocopy	retro_rnor_2456,