RetrogeneDB ID: retro_mmus_460

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:80383106..80385149(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000090637
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gle1
• Ensembl ID: ENSMUSG00000019715
• Aliases: None
• Description: GLE1 RNA export mediator (yeast) [Source:MGI Symbol;Acc:MGI:1921662]

Sequence

>retro_mmus_460
CTCCGCAACTCCAGCAAAGGCCGTCTGCACTACAACCAGGATGTTTTGGAAGAATGCAGATCTCTCCCCAAACTATCTTC
TTACTCTGGATGGGTGGTAGATCACATTCTACCCAACACCTTACGCCACACTCAAGAGAATGGTCCTTCCTCGGATAACC
CATCATCCTCTGGATCTGCTTCAGGCCTGTACCAATCCTCACTACTCAAGTCTCCTGTCAGAAGTACCCTACAATCACTC
TCACCCTCAACATCGAATGGAACCCAGAACACACATGACTCCCGGTTCACAGAACCTATTGCACTTCAGTCCTCTCCAGC
GATCAAAGTGGAAGGTTGTATCCGAATGTTCGAATCGGCATCTGGAATAAGAGCAACAGAGGGCCTGACGAAGTGGCAGG
AGGAGCAAGAAAGGAAGGTGCAAGCCTTCTCAGAGATGGCATCCGAACAGCTAAAGAAGTTTGACGAGCTGAAGGAGTTG
AAGATGAATAAGGAGTTACGGGACTTAGAGGAAGTGATGGAGAAGAGTATCAGAGAAGCCCTGGGTCATCAGGAGAAGCT
GAAAGCTGAGCATCACCACAGAGCCAAGATTCTCAAGCTAATGCTTCAAGAGGCAGAGCAGCGGCAGCGTGAGAAGCAGG
CAGAGCAGGAGCAGCTTCGAAAGGAGGAAGGCCAGGCCCGTCTGCGCAGCCTGTACACCCTGCAAGAGGAGGTCCTGCAG
CTCAATCAGCAGCTGGATGCCTCCAGTCAACACAAAGACCTGCTGAATGTGGACCTGGCTGCCTTCCAGACCCAGGGCAA
CCAGCTGTGTAGCGTCATCTCCGGCATCATTTGCAGCACTTTGGAGAGTGGCATTCCCACGGCCGAGAACCAAGCTGAGG
CCGAGCTGGCCCTGCAGGAAATGCAGGACCTCCTCTTGAGTTTGGAGCAGGAGATCACCAGAGCCTCTGAAGTGAAGAAG
AAGAACGAGGAGGAAGAGGCCCAAGTCAAGCGGCAGGAGTCACAGATGCAGCAGGGGCCAGGAGTTCCCACCCAGAGCTC
TGCACCCAGCCCAAGCCCAACAGGTTCGCAGAATGAAGACCTGCAGGGGAAGGTACAAGATAGTACACTGCAGTGGTACC
AGCAACTTCAGGATGCTTCCGCCAAATGTGTGTTGGCCTTTGAGGACCTGACCAGCAGCAAGGACAGTCAGACGAAAAAG
ATAAGGACGGATTTGCGGAAGGCAGCCACCATTCCAGTGAGCCAGATCTCCGGCATCTCAGGTTCAAAGCTGAAGGAGGT
CTTTGATAAGCTCCACAGTCTGCTCTCGGGAAAGCCTGTCCAATCTGGAGGGCGTTCCGTGTCTGTCACTCTTAACCCTC
AGGGGCTGGACTTTGTCCAGTACAAACTGGCAGAGAAATTTGTGAAACAAGGGGAGAAGGAAGTGGCCTCTCACCACGAA
GCGGCATTCCCCATTGCGGCGGTGGCTTCTGGTATCTGGATGCTCCACCCCAAAGTGGGAGACCTCATTCTTGCTCATCT
CCACAAGAAGTGTCCATACTCCGTTCCTTTCTACCCAGCTTTCAAGGAAGGGATGGCTTTGGAGGATTATCAACGGATGC
TTGGCTATCAAGTTGTGGATTCCAAGGTTGAGCGGCAGGAAAGCTTTCTGAAACGCATGTCTGGGATGATCCGTTTGTAT
GCCGCCATCATCCAGCTCCAGTGGCCATATGCAAACCGGCAGGAGGTTCATCCTCATGGCTTAAATCATGGCTGGCGCTG
GTTGGCACAGATCTTAAACATGGAGCCTCTCTCAGGTGTAACAGCCACTCTCCTGTTTGACTTTTTGGAGGTGTGTGGGA
ACGCCCTCATGAAGCAGAACCAGGTCCAGTTCTGGAAGATGATACTTTTCATCCAAGAGGACTACTTGCCCAGAATTGAG
GCCATCACGAGCTCAGGACAGATGGGCTCTTTCATACGTCTCAAGCAGTTCTTGGAGAAGTGTCTGCAACGCAGGGAGAT
TCCTGTCCCCAGAGGCTTTCTGACGCCCTCCTTCTGGTGCTCT

Alignment

ORF - retro_mmus_460 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.32 %
• Parental protein coverage: 97. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRYDREWLLRY-EDVLEECMSLPKLSSYSGWVVDHILPNTSGHTQESAPSSDNSPSSGSASGLYQSSLLK
          LR......L.Y..DVLEEC.SLPKLSSYSGWVVDHILPNT..HTQE..PSSDN..SSGSASGLYQSSLLK
Retrocopy LRNSSKGRLHYNQDVLEECRSLPKLSSYSGWVVDHILPNTLRHTQENGPSSDNPSSSGSASGLYQSSLLK

Parental  SPVRSSPQSPSPSSPNGTQSTHESPFTEPIAPQSSRAIKVEGCIRMYELAHRMRGTEGLRQWQEEQERKV
          SPVRS..QS.SPS..NGTQ.TH.S.FTEPIA.QSS.AIKVEGCIRM.E.A...R.TEGL..WQEEQERKV
Retrocopy SPVRSTLQSLSPSTSNGTQNTHDSRFTEPIALQSSPAIKVEGCIRMFESASGIRATEGLTKWQEEQERKV

Parental  RALSEMASEQLKRFDELKELKLHKEFQDLQEVMEKSTREALGHQEKLKEEHRHRAKILNLKLREAEQ-QR
          .A.SEMASEQLK.FDELKELK..KE..DL.EVMEKS.REALGHQEKLK.EH.HRAKIL.L.L.EAEQ.QR
Retrocopy QAFSEMASEQLKKFDELKELKMNKELRDLEEVMEKSIREALGHQEKLKAEHHHRAKILKLMLQEAEQRQR

Parental  VKQAEQEQLRKEEGQVRLRSLYSLQEEVLQLNQQLDASSQHKELLSVDLAAFQTRGNQLCGLISSIIRTT
          .KQAEQEQLRKEEGQ.RLRSLY.LQEEVLQLNQQLDASSQHK.LL.VDLAAFQT.GNQLC..IS.II..T
Retrocopy EKQAEQEQLRKEEGQARLRSLYTLQEEVLQLNQQLDASSQHKDLLNVDLAAFQTQGNQLCSVISGIICST

Parental  LESGYPTAENQAEAERALQEMRDLLSDLEQEITRASQVKKKHEEE-AKVKRQESQVQQGPAPPTQTSAPS
          LESG.PTAENQAEAE.ALQEM.DLL..LEQEITRAS.VKKK.EEE.A.VKRQESQ.QQGP..PTQ.SAPS
Retrocopy LESGIPTAENQAEAELALQEMQDLLLSLEQEITRASEVKKKNEEEEAQVKRQESQMQQGPGVPTQSSAPS

Parental  PSPVGAQNEDLQVKVQDSTMQWYQQLQDASAKCVLAFEDLTSSKDSQTKKIKMDLQKAATIPVSQISTIA
          PSP.G.QNEDLQ.KVQDST.QWYQQLQDASAKCVLAFEDLTSSKDSQTKKI..DL.KAATIPVSQIS.I.
Retrocopy PSPTGSQNEDLQGKVQDSTLQWYQQLQDASAKCVLAFEDLTSSKDSQTKKIRTDLRKAATIPVSQISGIS

Parental  GSKLKEIFDKIHSLLSGKPVQSGGRSVSVTLNPQGLDFVQYKLAEKFVKQGEEEVASHHEAAFPIAVVAS
          GSKLKE.FDK.HSLLSGKPVQSGGRSVSVTLNPQGLDFVQYKLAEKFVKQGE.EVASHHEAAFPIA.VAS
Retrocopy GSKLKEVFDKLHSLLSGKPVQSGGRSVSVTLNPQGLDFVQYKLAEKFVKQGEKEVASHHEAAFPIAAVAS

Parental  GIWMLHPKVGDLILAHLHKKCPYSVPFYPAFKEGMALEDYQRMLGYQVTDSKVEQQDNFLKRMSGMIRLY
          GIWMLHPKVGDLILAHLHKKCPYSVPFYPAFKEGMALEDYQRMLGYQV.DSKVE.Q..FLKRMSGMIRLY
Retrocopy GIWMLHPKVGDLILAHLHKKCPYSVPFYPAFKEGMALEDYQRMLGYQVVDSKVERQESFLKRMSGMIRLY

Parental  AAIIQLQWPYGNRQEAHPHGLNHGWRWLAQVLNMEPLSDVTATLLFDFLEVCGNALMKQYQVQFWKMILL
          AAIIQLQWPY.NRQE.HPHGLNHGWRWLAQ.LNMEPLS.VTATLLFDFLEVCGNALMKQ.QVQFWKMIL.
Retrocopy AAIIQLQWPYANRQEVHPHGLNHGWRWLAQILNMEPLSGVTATLLFDFLEVCGNALMKQNQVQFWKMILF

Parental  IKEDYFPRIEAITSSGQMGSFIRLKQFLEKCLQRREIPVPRGFLTTSFWRS
          I.EDY.PRIEAITSSGQMGSFIRLKQFLEKCLQRREIPVPRGFLT.SFW.S
Retrocopy IQEDYLPRIEAITSSGQMGSFIRLKQFLEKCLQRREIPVPRGFLTPSFWCS

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	0.12 RPM	47.29 RPM
SRP007412_cerebellum	0.00 RPM	67.00 RPM
SRP007412_heart	0.06 RPM	31.88 RPM
SRP007412_kidney	0.10 RPM	39.17 RPM
SRP007412_liver	0.00 RPM	33.51 RPM
SRP007412_testis	0.09 RPM	41.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_460 was not detected

EST

No EST(s) were mapped for retro_mmus_460 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_76680	1005 libraries	58 libraries	8 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_460 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_460 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000017640	1 retrocopy	retro_mmur_1261,
Myotis lucifugus	ENSMLUG00000007379	1 retrocopy	retro_mluc_171,
Mus musculus	ENSMUSG00000019715	2 retrocopies	retro_mmus_3505, retro_mmus_460 ,
Rattus norvegicus	ENSRNOG00000015237	1 retrocopy	retro_rnor_2323,