RetrogeneDB ID: retro_mmus_3084

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:123558795..123559599(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gm11232
• Ensembl ID: ENSMUSG00000066141
• Aliases: None
• Description: predicted gene 11232 [Source:MGI Symbol;Acc:MGI:3651439]

Sequence

>retro_mmus_3084
TTGAGTGAAACGCTAGTCGAGAAGCCTGGACATATGAATTTAGAGATGTCCACCCTGGCTCCTTCCAAGAGAAAGCAGCC
CCTAAACAAGAAGGCAGAAGACAAACAGCCCTCTGAGAGTCGGGGTAACAATGGCAGGAGTTCCAAGTCCTCTCCCATGG
GCAAAGAGAACACCTGGCCAAGTCGGGAGGCTAAGGTCTCCAGCCAGAAGCGATCTGGGCAAAGCTGGGCTGTCTCCTCC
TGCGGACCCCACAAGAGAAGCAGCAAGCTGGAGGAGAAGAGGAGGAACAGACCATCTCTCTCCAGAGAGAGAGGAAGGGA
CAAGCTGGGGTCCACCCACAAAAGAGACTCCTCGCACACAAAACTGCATGTAAAGGACCGAAGGTCCCAGCCAAGATCTC
CTGTGAGGACTCTGAAGCGCAGTCACTCTGGAGACAGCCGAGGTGCCCCGAACAACTCTGCCAAGAGGCGCAGACAGATT
TCTCCTCCAGAAGCCAGCTCATTACCAACATTCTCGCTGCTCATGTCCAGAGTCTTCACCAACGTGGATGCCTTGCAGGT
GACCCTGGACGACCTGCAAGCCCCCGGAGGTGCCTTCCTGCGTGTGCCCTCAAGCAGCACGGAGCCCAGTGTCTCGCAGC
GGGCCTGGCTCACTTGGCAACTGTCCCATGCAGGAGCCGCACTGCACTGGGCGCTTCACACAGTCAATTCCATCTTGACT
GCACAGGCCAGCCTGCCCAGATACACCTGGCCCCAAGGCTATTCCTTCACTGCTGACCCTAGACCCGTGCCCACCTCCAA
GATC

Alignment

ORF - retro_mmus_3084 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.25 %
• Parental protein coverage: 90.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNETPDEKPGHVKLEMSTQSSSKRMQPLDQKDKENQSSESWGNTGRSSKSSPKGKENTWPKSEVKVPSQK
          ..ET..EKPGH..LEMST...SKR.QPL..K....Q.SES.GN.GRSSKSSP.GKENTWP..E.KV.SQK
Retrocopy LSETLVEKPGHMNLEMSTLAPSKRKQPLNKKAEDKQPSESRGNNGRSSKSSPMGKENTWPSREAKVSSQK

Parental  KFQQSWAVSSCGPNKRSSKLKEKKRDKPSPSRERGRDKLVSTHRRDISHTKLHVRDQRPQPRSPVRTLKR
          ...QSWAVSSCGP.KRSSKL.EK.R..PS.SRERGRDKL.STH.RD.SHTKLHV.D.R.QPRSPVRTLKR
Retrocopy RSGQSWAVSSCGPHKRSSKLEEKRRNRPSLSRERGRDKLGSTHKRDSSHTKLHVKDRRSQPRSPVRTLKR

Parental  SRGGDSPDAPYHSAKRCRKPSLPEASLDLTFSQLMSRVFTNLSALQVTLDDLQAPGGAFLHVPSSSLEPT
          S..GDS..AP..SAKR.R..S.PEAS...TFS.LMSRVFTN..ALQVTLDDLQAPGGAFL.VPSSS.EP.
Retrocopy SHSGDSRGAPNNSAKRRRQISPPEASSLPTFSLLMSRVFTNVDALQVTLDDLQAPGGAFLRVPSSSTEPS

Parental  VSQRAWLTWQLYHAGATVHWALQTVNSILNSQASLPRHTCPQGYSFTADPRTVPTSSL
          VSQRAWLTWQL.HAGA..HWAL.TVNSIL..QASLPR.T.PQGYSFTADPR.VPTS..
Retrocopy VSQRAWLTWQLSHAGAALHWALHTVNSILTAQASLPRYTWPQGYSFTADPRPVPTSKI

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.04 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.05 RPM	0.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3084 was not detected

EST

No EST(s) were mapped for retro_mmus_3084 retrocopy.

TSS

No TSS is located nearby retro_mmus_3084 retrocopy 5' end.

Lab

retro_mmus_3084 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3084 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000066141	6 retrocopies	retro_mmus_3084 , retro_mmus_371, retro_mmus_372, retro_mmus_373, retro_mmus_374, retro_mmus_375,