RetrogeneDB ID: retro_mmus_371

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:151182627..151183431(+)
• 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_371
TTGAGTGAAACGCTAGTCGAGAAGCCTGAACATATGAATTTAGAGATGTCCATCCTGGCTCCTTCCAAGAGAAAGCAGCT
CCTAGACAAGAAGGCAGAAGACAAACAGCCCCCTGAGAGTCGGGGTAACAATGGCAGGAGTTCCAAGTCCTCTCCCATGG
GCAAAGACAACACCTGGCCAAGTCCGGAGGCTAAGGTCCCCAGTCAGAAGCGATCTGGGCAAAGCTGGGCTGTCTCCTCC
TGCGGACCCCACAAGAGAAGCAGCAAGCTGGAGGACAAGAGGAGGAACAGACCATCTCGCTTCAGAGAGAGAGGAAGGGA
CAAGCCGGGGTCCACCCACAAAAGAGATTCCTCGCACACAAAACTGCATGTAAAGGACCGAAGGTCCCAGCCAAGATCTC
CTGTGAGGACTCTGAAGCGCAGTCGCTCTGGAGACAGGCAAGGTGCCCCGCACAACTCTGCCAAGAGGCACAGACAGACT
TCTCCTCCAGAAGCCAGCTCATTACCAACATTCTCGCTGCTCATGTCCAGAGTCTTCACCAACGTGGATGCCTTGCAGGT
GAGCCTGGACGACCTGCAAGCCCCCGGAGGTGCCTTCCTGCGTGTGCCCTCAAGCAGCACGGAGCCCATTGTCTTGCAGC
GGGCCTGGCTCACTTGGCAACTGTCCCATGCAGGAGCCGCACTGCACTGGGCGCTTCACACAGTCAAGTCCATCTTGACT
TCGCAAGCCAGCCTGCCCAGATACACCTGGCCCCAAGGCTATTCCTTCACTGCTGACCCTAGACCCGTGCCCACCTCCAA
GATC

Alignment

ORF - retro_mmus_371 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.27 %
• 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.GN.GRSSKSSP.GK.NTWP..E.KVPSQK
Retrocopy LSETLVEKPEHMNLEMSILAPSKRKQLLDKKAEDKQPPESRGNNGRSSKSSPMGKDNTWPSPEAKVPSQK

Parental  KFQQSWAVSSCGPNKRSSKLKEKKRDKPSPSRERGRDKLVSTHRRDISHTKLHVRDQRPQPRSPVRTLKR
          ...QSWAVSSCGP.KRSSKL..K.R..PS..RERGRDK..STH.RD.SHTKLHV.D.R.QPRSPVRTLKR
Retrocopy RSGQSWAVSSCGPHKRSSKLEDKRRNRPSRFRERGRDKPGSTHKRDSSHTKLHVKDRRSQPRSPVRTLKR

Parental  SRGGDSPDAPYHSAKRCRKPSLPEASLDLTFSQLMSRVFTNLSALQVTLDDLQAPGGAFLHVPSSSLEPT
          SR.GD...AP..SAKR.R..S.PEAS...TFS.LMSRVFTN..ALQV.LDDLQAPGGAFL.VPSSS.EP.
Retrocopy SRSGDRQGAPHNSAKRHRQTSPPEASSLPTFSLLMSRVFTNVDALQVSLDDLQAPGGAFLRVPSSSTEPI

Parental  VSQRAWLTWQLYHAGATVHWALQTVNSILNSQASLPRHTCPQGYSFTADPRTVPTSSL
          V.QRAWLTWQL.HAGA..HWAL.TV.SIL.SQASLPR.T.PQGYSFTADPR.VPTS..
Retrocopy VLQRAWLTWQLSHAGAALHWALHTVKSILTSQASLPRYTWPQGYSFTADPRPVPTSKI

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	0.04 RPM	0.00 RPM
SRP007412_heart	0.06 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_371 was not detected

EST

No EST(s) were mapped for retro_mmus_371 retrocopy.

TSS

No TSS is located nearby retro_mmus_371 retrocopy 5' end.

Lab

retro_mmus_371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_371 has 0 orthologous retrocopies within eutheria group .

---

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,