RetrogeneDB ID: retro_mmus_372

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:151192435..151193242(+)
• 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_372
TTGAGTGAAACGCTAGTCGAGAAGCCTGAACATATGAATTTAGAGATGTCCATCCTGGCTCCTTCCAAGAGAGAGCAGCT
CCTAGACAAGAAGGCAGAAGACAAACAGCCCCCTGAGAGTCGGTGTAACAATGGCAGGAGTTCCAAGTCCTCTCCCATGG
GCAAAGAGAACACCTGGCCAAGTCGGGAGGCTAAGGTCCCCAGTCAGAAGCGATCTGGGCAAAGCTGGGCTGTCTCCTCC
TGCGGACCCCACAAGAGAAGCAGCAAGCTGGAGGACAAGAGGAGGAACAGACCATCTCGCTTCAGAGAGAGAGGAAGGGA
CAAGCCGGGGTCCACCCACAAAAGAGATTCCTCGCACACAAAACTGCATGTAAAGGACCAAAGGTCCCAGCCAAGATCTC
CTGTGAGGACTCTGAAGCGCAGTCGCTCTGGAGACAGGCAAGGTGCCCCGCACAACTATGCCAAGAGACGCAGACAGACA
TTTCCTCCAGAAGCCAGCTGCTCATTACCAACATTCTCGCTGCTCATGTCCAGAGTCTTCACCAACGTGGATGCCTTGCA
GGTGAGCCTGGACGACCTGCAAGCCCCCGGAGGTGCCTTCCTGCGTGTGCCCTCAAGCAGCACGGAGCCCAGTGTCTCGC
AGCGGGCCTGGCTCACTTGGCAACTGTCCCATGCAGGAGCAGCACTGCACTGGGCGCTTCACACAGTCAATTCCATCTTG
ACTGCGCAGGCCAGCCTGCCCAGATACATCTGGCCCCAAGGCTATTCCTTCACTGCTGACCCTAGACCCGTGCCCACCTC
CAAGATC

Alignment

ORF - retro_mmus_372 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71. %
• Parental protein coverage: 90.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNETPDEKPGHVKLEMSTQSSSKRMQPLDQKDKENQSSESWGNTGRSSKSSPKGKENTWPKSEVKVPSQK
          ..ET..EKP.H..LEMS....SKR.Q.LD.K....Q..ES..N.GRSSKSSP.GKENTWP..E.KVPSQK
Retrocopy LSETLVEKPEHMNLEMSILAPSKREQLLDKKAEDKQPPESRCNNGRSSKSSPMGKENTWPSREAKVPSQK

Parental  KFQQSWAVSSCGPNKRSSKLKEKKRDKPSPSRERGRDKLVSTHRRDISHTKLHVRDQRPQPRSPVRTLKR
          ...QSWAVSSCGP.KRSSKL..K.R..PS..RERGRDK..STH.RD.SHTKLHV.DQR.QPRSPVRTLKR
Retrocopy RSGQSWAVSSCGPHKRSSKLEDKRRNRPSRFRERGRDKPGSTHKRDSSHTKLHVKDQRSQPRSPVRTLKR

Parental  SRGGDSPDAPYHSAKRCRKPSLPEASLDL-TFSQLMSRVFTNLSALQVTLDDLQAPGGAFLHVPSSSLEP
          SR.GD...AP...AKR.R....PEAS..L.TFS.LMSRVFTN..ALQV.LDDLQAPGGAFL.VPSSS.EP
Retrocopy SRSGDRQGAPHNYAKRRRQTFPPEASCSLPTFSLLMSRVFTNVDALQVSLDDLQAPGGAFLRVPSSSTEP

Parental  TVSQRAWLTWQLYHAGATVHWALQTVNSILNSQASLPRHTCPQGYSFTADPRTVPTSSL
          .VSQRAWLTWQL.HAGA..HWAL.TVNSIL..QASLPR...PQGYSFTADPR.VPTS..
Retrocopy SVSQRAWLTWQLSHAGAALHWALHTVNSILTAQASLPRYIWPQGYSFTADPRPVPTSKI

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	0.10 RPM	0.04 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_372 was not detected

EST

2 EST(s) were mapped to retro_mmus_372 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BB842869	151192375	151192762	100	387	0	387
BB843324	151192375	151192739	100	360	0	356

TSS

No TSS is located nearby retro_mmus_372 retrocopy 5' end.

Lab

retro_mmus_372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_372 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,