RetrogeneDB ID: retro_mmus_3546

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:152565211..152565641(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081993
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rab7
• Ensembl ID: ENSMUSG00000079477
• Aliases: Rab7, Rab7a
• Description: RAB7, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:105068]

Sequence

>retro_mmus_3546
ATGACCTGTAGGAAGAAAGTGCTGCTGAAGGGCATGATTCTGGGAGATTATGGTATTGGAAAGGCATATCTCAGGAACCA
GCATGTGCATAAGCTCAGTAGCCAGTACAAAGCCACATACTTTCTCACCAAGGACGTGATGGTGGATTACAGAATTTTTA
CCATGCATATCTGGGACACATCTGGTCAAAAATGGTTCCAATTTCTTGGTGTGGCCTTCTACAGAGGTTCAGATTGCATT
CTGGTGTTTGATGTGACTGCCTCCAACACATTCACAACCCTTGACAGCTAGAGAGACAAACTTCTTATTCAGGCTAGCCC
CTGGGATCCCAAGAACTTCCCTTTTGTTGTGTTTGGAAACAAGATTGGCCTCAAAGACAAGGCAAGTGACCACAAAGAGA
GCACACAGGTTTGGTGCTACAAAAACAAGC

Alignment

ORF - retro_mmus_3546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.44 %
• Parental protein coverage: 71.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERF
          MT.RKKVLLK..ILGD.G.GK..L.NQ.V.K..S.QYKAT....FLTK.VMVD.R..TM.IWDT.GQ..F
Retrocopy MTCRKKVLLKGMILGDYGIGKAYLRNQHVHK-LSSQYKATY---FLTKDVMVDYRIFTMHIWDTSGQKWF

Parental  QSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEN-RQVATKRA
          Q.LGVAFYRG.DC..LVFDVTA.NTF.TLDS.RD..LIQASP.DP.NFPFVV.GNKI.L...RQV.TKRA
Retrocopy QFLGVAFYRGSDC-ILVFDVTASNTFTTLDS*RDKLLIQASPWDPKNFPFVVFGNKIGLKD>RQVTTKRA

Parental  QAWCYSKNN
          ......K..
Retrocopy HRFGATKTS

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	155.20 RPM
SRP007412_cerebellum	0.00 RPM	138.69 RPM
SRP007412_heart	0.00 RPM	129.72 RPM
SRP007412_kidney	0.00 RPM	191.40 RPM
SRP007412_liver	0.00 RPM	128.73 RPM
SRP007412_testis	0.41 RPM	24.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3546 was not detected

EST

No EST(s) were mapped for retro_mmus_3546 retrocopy.

TSS

No TSS is located nearby retro_mmus_3546 retrocopy 5' end.

Lab

retro_mmus_3546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3546 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000365	1 retrocopy	retro_chof_13,
Felis catus	ENSFCAG00000022971	2 retrocopies	retro_fcat_661, retro_fcat_76,
Meleagris gallopavo	ENSMGAG00000007208	1 retrocopy	retro_mgal_7,
Myotis lucifugus	ENSMLUG00000008454	1 retrocopy	retro_mluc_1641,
Mustela putorius furo	ENSMPUG00000017333	1 retrocopy	retro_mputfur_1169,
Mus musculus	ENSMUSG00000079477	2 retrocopies	retro_mmus_3339, retro_mmus_3546 ,
Oryctolagus cuniculus	ENSOCUG00000001645	1 retrocopy	retro_ocun_259,
Pongo abelii	ENSPPYG00000013431	1 retrocopy	retro_pabe_90,
Rattus norvegicus	ENSRNOG00000012247	1 retrocopy	retro_rnor_2779,
Sarcophilus harrisii	ENSSHAG00000016787	1 retrocopy	retro_shar_65,