RetrogeneDB ID: retro_mmus_1090

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:33596037..33596776(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mlf2
• Ensembl ID: ENSMUSG00000030120
• Aliases: Mlf2, AI256856, AU018944, C77284
• Description: myeloid leukemia factor 2 [Source:MGI Symbol;Acc:MGI:1353554]

Sequence

>retro_mmus_1090
ATGTTCTGCTTCATGAGAGACGTAGAGCCGGAGGATTCCATTTTCCTGATGGACCCCTTCGCAATTCACCATCAGTATTG
AGCTGCATGCTGTCAGGTGGCTTTGGATATAGCCCCTTCCTGAACAGCACAGATGGTAACATGCCAACAATCAGGCCTGC
CAGCTGCAGAATTCAGGCTGGGGCTGTCTCTCCTTTGGAATGTTGGTGATGTCCAGAGGCTTTGTGGATATGTTTGGGAT
GATGAACGACATGATTGGAAACATGGAGCACATGGCTGACAGAGGCAACTGCCAGACCTTCTCCTCCTCCACTGTCATCT
CCTACCCCAACACTGGGGATGGTGCCCTCAAGGTTTACCAGGAGATATCTGAGAGGTGCTCAGCCCCAGGCGGGATCCGG
GAGACACAGAGGACTGTCCGTGACTCAGACAGTGGTCTAAAGCAGAAGTCCACTGGACATTACATTTGAGATAGGGCTTA
CATCTTCCAGCACTCCGGAAACCACTGCACAGGGGACCTGGAAGAGCAGCAGAACTACATCAACCTGGATGAAACTAAAG
CAGCAGCGTTTGATGATGAATGGAGAAGGGAGACATCCCGATTCAGACAGCAACATCCTCTGGAATTTCGATGGCATAAG
GCATCTGTGGGTGGGTGGTGTAAGGCTGAAGGGCCTCCCTGCCTGGCTATCCAGGGACAGGAGGACTCCCATTCCTGAAA
GTCAAGTCACTATGACTGG

Alignment

ORF - retro_mmus_1090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFRFMRDVEPEDPMFLMDPFAIHRQH-MSRMLSGGFGYSPFLSITDGNMPATRPASRRMQAGAVSP-FGM
          MF.FMRDVEPED..FLMDPFAIH.Q...S.MLSGGFGYSPFL..TDGNMP..RPAS.R.QAGAVSP.FGM
Retrocopy MFCFMRDVEPEDSIFLMDPFAIHHQY<LSCMLSGGFGYSPFLNSTDGNMPTIRPASCRIQAGAVSP<FGM

Parental  LGMSGGFMDMFGMMNDMIGNMEHMAAGGNCQTFSSSTVISYSNTGDGAPKVYQETSEMRSAPGGIRETRR
          L.MS.GF.DMFGMMNDMIGNMEHMA..GNCQTFSSSTVISY.NTGDGA.KVYQE.SE..SAPGGIRET.R
Retrocopy LVMSRGFVDMFGMMNDMIGNMEHMADRGNCQTFSSSTVISYPNTGDGALKVYQEISERCSAPGGIRETQR

Parental  TVRDSDSGLEQMSIGHHIRDRAHILQRSRNHRTGDQEERQDYINLDESEAAAFDDEWRRETSRYRQQRPL
          TVRDSDSGL.Q.S.GH.I.DRA.I.Q.S.NH.TGD.EE.Q.YINLDE..AAAFDDEWRRETSR.RQQ.PL
Retrocopy TVRDSDSGLKQKSTGHYI*DRAYIFQHSGNHCTGDLEEQQNYINLDETKAAAFDDEWRRETSRFRQQHPL

Parental  EFRRHEASVGGGRRAEGPPRLAIQGPEDSPSRQSRRYDW
          EFR.H.ASVGG...AEGPP.LAIQG.EDS.S..S..YDW
Retrocopy EFRWHKASVGGWCKAEGPPCLAIQGQEDSHS*KSSHYDW

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	259.09 RPM
SRP007412_cerebellum	0.00 RPM	240.38 RPM
SRP007412_heart	0.00 RPM	146.16 RPM
SRP007412_kidney	0.00 RPM	146.59 RPM
SRP007412_liver	0.00 RPM	129.31 RPM
SRP007412_testis	0.05 RPM	29.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1090 was not detected

EST

No EST(s) were mapped for retro_mmus_1090 retrocopy.

TSS

No TSS is located nearby retro_mmus_1090 retrocopy 5' end.

Lab

retro_mmus_1090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1090 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000758	2 retrocopies	retro_dnov_1602, retro_dnov_649,
Echinops telfairi	ENSETEG00000014471	2 retrocopies	retro_etel_1236, retro_etel_233,
Microcebus murinus	ENSMICG00000010652	1 retrocopy	retro_mmur_449,
Monodelphis domestica	ENSMODG00000018113	1 retrocopy	retro_mdom_324,
Mus musculus	ENSMUSG00000030120	1 retrocopy	retro_mmus_1090 ,
Otolemur garnettii	ENSOGAG00000005976	1 retrocopy	retro_ogar_232,
Procavia capensis	ENSPCAG00000001026	1 retrocopy	retro_pcap_326,
Ictidomys tridecemlineatus	ENSSTOG00000009908	1 retrocopy	retro_itri_1707,