RetrogeneDB ID: retro_mmus_3505

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:107542590..107543742(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000055700
• 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_3505
CAGGAAATGTAGGATCACCTCTCAAAGTTGGAGCAGGAGATCACTAGAGCCTCTAAAATGAACAGGAAGGATGAAGAGGA
GGCCCGGGTCAAGCTGCAGGAGTCAAAGATACACCAGAGACCAGGGGCTCCCACCCAGACCTCTGTACCAAGCCCAAGCC
CAAGCTCAGTAGTAACGCAGAATGAAGGCCTGCAAGTGAATGTACAAGACAGTACAATGCAGTGGTACCATCAAATTCAG
GATACTTGTGCCAAATGTGTGCTGGCCTTTGAGGACCTGACCAGCAGCAAGAACAGTCAGACCAAAAGGATAAAAATGGA
CTTGCAGAATGCAGCCACCATCCCAGTGAGTCAGATCTCTACCATCTCAGGTTCAAAGCTGAAGGAGGTCTTTGATGAGA
TCCATAGCCTGCTCTCTGGAAAGCCTGTCCAATCAGGTGGGCGTTCTGTGTCTGTTGCTCTTAACCCACAGGGGCTGAAA
TTTGTCCAGTACAAACTGGCAGAGAATTTTGTGAAACAAGGAGAGGAGAAAGTGGCCTCTCACCATGAAGCAGCATTCCC
CATTGCGGTGGTGGCATCTGGTATCTGGAAGCTCCACCCTAAAGTGGGAGGCCTCATTCTCGCTCATCTCCACAAGAAGT
GTCCGTACTCCGTTCCTTACTACCCAGCTTTCAAGGAAGGGATGGATTTGGAGGAATATCACCAGATGCTTGGCTACCAA
GTGATAGATTCCAAGGTTGAGCAACAGGAGAGCTTTATAAAACGAATGTCTGGGATGATCCGTTTATATGCCGCCATCAT
CCAGCTCCAGTGGCCATATGGAAACCGTCAGGAGGCTCATCCTCATGGCTTAAATCACGGCTGGCGCTGGTTGGCACAGA
TCTTAAACGTGGAGCCTCTCTCAGATGTGACAGCCACTCTCCTGTTTGATTTCTTGGAGGTGTGTGGGAATGCCCTCCTG
AAGCAGTACCAAGTCCAGTTCTGGAAAATGATACAACTCATCAAAGAGGACTACTTGCCCAGAATTGAAGCCATCACGAG
CCCAGGACAGATGGGCTCTTTGATACATCTGAAGCAGTTCTTGGATAAATGTCTGCAACGCAGGAATATTCCTGTTCCCA
GAGGCTTTCTGACTGCCTCCTTCTGGCAGTCT

Alignment

ORF - retro_mmus_3505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 54.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEMRDLLSDLEQEITRASQVKKKHEEEAKVKRQESQVQQGPAPPTQTSAPSPSP--VGAQNEDLQVKVQD
          QEM.D.LS.LEQEITRAS....K.EEEA.VK.QES...Q.P..PTQTS.PSPSP..V..QNE.LQV.VQD
Retrocopy QEM*DHLSKLEQEITRASKMNRKDEEEARVKLQESKIHQRPGAPTQTSVPSPSPSSVVTQNEGLQVNVQD

Parental  STMQWYQQLQDASAKCVLAFEDLTSSKDSQTKKIKMDLQKAATIPVSQISTIAGSKLKEIFDKIHSLLSG
          STMQWY.Q.QD..AKCVLAFEDLTSSK.SQTK.IKMDLQ.AATIPVSQISTI.GSKLKE.FD.IHSLLSG
Retrocopy STMQWYHQIQDTCAKCVLAFEDLTSSKNSQTKRIKMDLQNAATIPVSQISTISGSKLKEVFDEIHSLLSG

Parental  KPVQSGGRSVSVTLNPQGLDFVQYKLAEKFVKQGEEEVASHHEAAFPIAVVASGIWMLHPKVGDLILAHL
          KPVQSGGRSVSV.LNPQGL.FVQYKLAE.FVKQGEE.VASHHEAAFPIAVVASGIW.LHPKVG.LILAHL
Retrocopy KPVQSGGRSVSVALNPQGLKFVQYKLAENFVKQGEEKVASHHEAAFPIAVVASGIWKLHPKVGGLILAHL

Parental  HKKCPYSVPFYPAFKEGMALEDYQRMLGYQVTDSKVEQQDNFLKRMSGMIRLYAAIIQLQWPYGNRQEAH
          HKKCPYSVP.YPAFKEGM.LE.Y..MLGYQV.DSKVEQQ..F.KRMSGMIRLYAAIIQLQWPYGNRQEAH
Retrocopy HKKCPYSVPYYPAFKEGMDLEEYHQMLGYQVIDSKVEQQESFIKRMSGMIRLYAAIIQLQWPYGNRQEAH

Parental  PHGLNHGWRWLAQVLNMEPLSDVTATLLFDFLEVCGNALMKQYQVQFWKMILLIKEDYFPRIEAITSSGQ
          PHGLNHGWRWLAQ.LN.EPLSDVTATLLFDFLEVCGNAL.KQYQVQFWKMI.LIKEDY.PRIEAITS.GQ
Retrocopy PHGLNHGWRWLAQILNVEPLSDVTATLLFDFLEVCGNALLKQYQVQFWKMIQLIKEDYLPRIEAITSPGQ

Parental  MGSFIRLKQFLEKCLQRREIPVPRGFLTTSFWRS
          MGS.I.LKQFL.KCLQRR.IPVPRGFLT.SFW.S
Retrocopy MGSLIHLKQFLDKCLQRRNIPVPRGFLTASFWQS

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	47.29 RPM
SRP007412_cerebellum	0.00 RPM	67.00 RPM
SRP007412_heart	0.00 RPM	31.88 RPM
SRP007412_kidney	0.00 RPM	39.17 RPM
SRP007412_liver	0.00 RPM	33.51 RPM
SRP007412_testis	10.70 RPM	41.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3505 was not detected

EST

No EST(s) were mapped for retro_mmus_3505 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_154887	1063 libraries	6 libraries	1 library	1 library	1 library
TSS #2	TSS_154888	1066 libraries	3 libraries	1 library	1 library	1 library

The graphical summary, for retro_mmus_3505 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_3505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3505 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,