RetrogeneDB ID: retro_mmus_3006

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:18509975..18511478(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mtmr2
• Ensembl ID: ENSMUSG00000031918
• Aliases: Mtmr2, 6030445P13Rik
• Description: myotubularin related protein 2 [Source:MGI Symbol;Acc:MGI:1924366]

Sequence

>retro_mmus_3006
GCTTCCACTTCTCATTCAGAGAACTCGGTGCATAGCAAATCAGCTTCTGCTATATCATCAGATTCCATTTCAACTTCTGT
AGACAACTTTTCTCGTGATTTGAGGGTCCTGAGGGAGTCAAAGAAGTTAGCAGAAATGGAGGAACCAGCCCTGCTTCCAG
GAAAGAGCATTAAAGATATGGCCAAAGATGTGACTTACATATGTCCATTCACTGGTGCTGTACGAGGAACGCTGACTGTC
ACAAATTACAGATTATATTTCACGAGCATGGAGAAGGACCCCCTATTTGTTCTAGATGCTTCTCTTGGAGTGATAAGTAG
AGTAGAAAAGATTGGTGGTGCATCTAGCAGAGGTGAAAACTCTTATGGCCTTGAAACTGTGTGCAAGGATATCAGGAACT
TACGATTTGCTCATAAACCGGAGGGGCGAACAAGAAGATCCATATTTGAGAATCTAATGAAATATGCATTTCCTGTGTCT
AATGGCTTGCCTCTTTTTGCTTTTGAGTATAAAGAAGTATTCCCCGAAAATAGGTGGAAACTGTATGACCCTCTTCTAGA
GTACAGAAGTCAGGGAATTCCAAAAGAATGCTGGAGAATAACAAAGATAAATGAACTCTATGAACTCTGTGACACATATT
CTGCCCTCTTGGTTGTGCCAGCAAACATTCCTGATGAGAAGCTAAAGAGAGTGGCATCCTTTAGATCACGGGGCTGGATC
TCAGTTGCATCCTGGATTCATCCTGAAAGTCAAGCCACAGTCACTCGCTGCAGCCAGCCCATGGTTGGAGTGAGTGGGAA
GCAAAGCAAAGAGGATGAAAAGTACCTTCAGGCTATCATGGACTCCAATGCCCAGTCTCACAAAATATTTACATTTGATG
CTCAGCCAAGTCTCAGTGCTGTTGCCAATAAGGCAAAGGGGAGAGGTTATGAAAGTAAAGATGCCTATCAAAATGCAGAA
CTCATTTTTCTGGATATTCATAATATCGATGTTATGAGAGAATCATTACGGAAGCTTAAGGAGACTGTGTACCCCAACAT
TGAAGAAACTCACTGGTTGTCTAACTTAGAATCTACACACTGGCTGGAACACATTAAGCTCATTCTTACAGGGGCTCTTA
GGATTGCTGGCAAGGTCGAGTCTGGGAAGACGTCTGTGGTGGTAAACTGCATTGATGGATGGGATCGCACAGCTCAGCTC
ACTTCCCTGGCCATGGTCATGTTGAATGGATACTACCGAACCATACGAGGATTTGAAGTCCTTGTGGAGGAAGAATGGCT
GAGCTTTGGACATAGATTCCAACTAAGAGTTGGCCATGGAGATAAGAACCATGCTGATGCAGACAGATCACCTGTTTTCC
TTTAGTTTATTGACTGTGTCTGGCAAATGACAAGACAGTTCCCTACTGCATTTGAATTCAATGAGTATTTCCTCATTACC
ATCCTGGACCACTTGTACAGCTCTTTATTTGGAACATTCCTTTGTACTTGCCAAAAGAGCAGA

Alignment

ORF - retro_mmus_3006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.82 %
• Parental protein coverage: 77.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASTSHSENSVHTKSASAISSDSISTSADNFSPDLRVLREANKLAEMEEPALLPGENIKDMAKDVTYICPF
          ASTSHSENSVH.KSASAISSDSISTS.DNFS.DLRVLRE..KLAEMEEPALLPG..IKDMAKDVTYICPF
Retrocopy ASTSHSENSVHSKSASAISSDSISTSVDNFSRDLRVLRESKKLAEMEEPALLPGKSIKDMAKDVTYICPF

Parental  TGAVRGTLTVTSYRLYFKSMERDPPFVLDASLGVISRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKP
          TGAVRGTLTVT.YRLYF.SME.DP.FVLDASLGVISRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKP
Retrocopy TGAVRGTLTVTNYRLYFTSMEKDPLFVLDASLGVISRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKP

Parental  EGRTRRSIFENLMKYAFPVSNGLPLFAFEYKEVFPENGWKLYDPLLEYRRQGIPNESWRITKINERYELC
          EGRTRRSIFENLMKYAFPVSNGLPLFAFEYKEVFPEN.WKLYDPLLEYR.QGIP.E.WRITKINE.YELC
Retrocopy EGRTRRSIFENLMKYAFPVSNGLPLFAFEYKEVFPENRWKLYDPLLEYRSQGIPKECWRITKINELYELC

Parental  DTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATVTRCSQPMVGVSGKRSKEDEKYLQAIM
          DTY.ALLVVPANIPDE.LKRVASFRSRG.I.V.SWIHPESQATVTRCSQPMVGVSGK.SKEDEKYLQAIM
Retrocopy DTYSALLVVPANIPDEKLKRVASFRSRGWISVASWIHPESQATVTRCSQPMVGVSGKQSKEDEKYLQAIM

Parental  DSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPTIEET
          DSNAQSHKIF.FDA.PS..AVANKAKG.GYES.DAYQNAEL.FLDIHNI.VMRESLRKLKE.VYP.IEET
Retrocopy DSNAQSHKIFTFDAQPSLSAVANKAKGRGYESKDAYQNAELIFLDIHNIDVMRESLRKLKETVYPNIEET

Parental  HWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHCSDGWDRTAQLTSLAMLMLDGYYRTIRGFEV
          HWLSNLESTHWLEHIKLIL.GALRIA.KVESGKTSVVV.C.DGWDRTAQLTSLAM.ML.GYYRTIRGFEV
Retrocopy HWLSNLESTHWLEHIKLILTGALRIAGKVESGKTSVVVNCIDGWDRTAQLTSLAMVMLNGYYRTIRGFEV

Parental  LVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLF
          LVE.EWLSFGHRFQLRVGHGDKNHADADRSPVFL.FIDCVWQMTRQFPTAFEFNEYFLITILDHLYS.LF
Retrocopy LVEEEWLSFGHRFQLRVGHGDKNHADADRSPVFL*FIDCVWQMTRQFPTAFEFNEYFLITILDHLYSSLF

Parental  GTFLCNSEQQR
          GTFLC.....R
Retrocopy GTFLCTCQKSR

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	0.07 RPM	42.15 RPM
SRP007412_cerebellum	0.00 RPM	46.98 RPM
SRP007412_heart	0.06 RPM	15.63 RPM
SRP007412_kidney	0.10 RPM	39.89 RPM
SRP007412_liver	0.00 RPM	23.81 RPM
SRP007412_testis	0.05 RPM	59.55 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3006 was not detected

EST

No EST(s) were mapped for retro_mmus_3006 retrocopy.

TSS

No TSS is located nearby retro_mmus_3006 retrocopy 5' end.

Lab

retro_mmus_3006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3006 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000031918	3 retrocopies	retro_mmus_3004, retro_mmus_3005, retro_mmus_3006 ,
Nomascus leucogenys	ENSNLEG00000007138	1 retrocopy	retro_nleu_2239,