RetrogeneDB ID: retro_mmus_174

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:61808883..61810425(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000089992
• Aliases: G6pd2, G6pdx-ps1, Gpd-2, Gpd2
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: G6pdx
• Ensembl ID: ENSMUSG00000031400
• Aliases: G6pdx, G28A, G6pd, Gpdx
• Description: glucose-6-phosphate dehydrogenase X-linked [Source:MGI Symbol;Acc:MGI:105979]

Sequence

>retro_mmus_174
ATGGCAGAGCAGGTGACCCTAAGCCGGACCCAAGTGTGTGGGATCCTGAGGGAAGAGTTGTACCAAAATGATGCCTTCCA
CCAAGCTGATACACACATATTTATCATCATGGGTGCATCGGGTGACCTGGCCAAGAAGAAGATCTATCCCACCATCTGGT
GGCTGTTCCGGGATGGTCTTCTACCCAAAGAAACCTTCATTGTGGGCTATGCCCGCTCACAACTCACAGTGGATGACATC
CAAAAGCAGAGTGAGCCCTTCTTTAAGGCCACTCCAGAAGAAAGACCCAAGCTGGAGGAGTTCTTCACGCGTAACTCCTA
TGTAGTTGGCCAGTATGATGATCCAGCCTCCTATAAGCACCTCAACAGCTACATTAATGCCCTGCACCAGGGGATGCAGG
CCAACCATCTATTCTACCTGGCCTTGCCCCCCACAGTCTATGAAGCAGTCACCAAGAACATTCAAGAGACCTGCATGAGT
CAGACAGGCTTTAACCGCATCATAGTGGAGAAACCCTTCGGGAGAGACCTGCAGAGCTCCAATCAATTGTCTAACCACAT
CTCCTCTCTTTTCCGTGAAGACCAGATCTACCGCATTGACCACTACCTGGACAAAGAGATGGTCCAGAACCTCATGGTGC
TGAGGTTTGCTAACAGGATCTTTGGCCCTATCTGGAATGGAGACAACATTGCTTGTGTGATCCTCACATTTAAAGAGCCC
TTTGGTACTGAGGGTCGTGGGGGCTATTTTGATGAATTTGGGATCATCAGGGATGTTATGCAGAGCCACCTCCTGCAGAT
GTTGTGTCTGGTGGCCATGGAAAAGCCTGCTACCACAGATTCAGATGATGTCCGTAATGAGAAGGTCAAAGTGTTGAAAC
GTATCTCAGAGGTGGAAACTGACAATGTGATCCTTGGCCAGTATGTGGGGAACCCCAATGGAGAAGGAGAAGCTGCCAAT
GGATACTTAGATGACCCCACAGTACCCCGTGGGTCCACAACTGCCACCTTTGCTGCAGCTGTCCTCTATGTGAAGAATGA
ACGGTGGGATGGGGTACCCTTCATACTGCGCTGTGGCAAAGCCCTGAATGAACGCAAAGCTGAAGTGAGACTGCAATTCC
GAGATATACCAGGCGACATCTTCCACCAGAAGTGCAAGCGTAATGAGCTGGTCATCCGTATGCAGCCCAATGAGGCAGTA
TACACAACGATGATGACCAAGAAGCCTGGCATGTTCTTTAACCCTGAGGAGTCGGAGCTGGACCTAACTTATGGCAACAA
ATACAAGAATGTGAAGCTCCCTGGTGCCTATGAACGCCTCATCCTGGATGTCTTCTGTGGGTGCCAGATGCACTTTGTCC
GTACTGATGAACTCAGGGAAGGCTGGCGTATCTTCACACCACTGCTGCACAAGATTGAACGAGAAAAGCCCCAGCCCTTC
CCCTATGTATATGGCAGCCGTGGCCCCACAGAGGCAGATGAGCTGATGAGGAGAGTGGGCTTCCAGTACAAGGGTACCTA
CAAGGGTACTCACAAGCACTGA

Alignment

ORF - retro_mmus_174 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.2 %
• Parental protein coverage: 99.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEQVALSRTQVCGILREELYQGDAFHQADTHIFIIMGASGDLAKKKIYPTIWWLFRDGLLPEDTFIVGY
          MAEQV.LSRTQVCGILREELYQ.DAFHQADTHIFIIMGASGDLAKKKIYPTIWWLFRDGLLP..TFIVGY
Retrocopy MAEQVTLSRTQVCGILREELYQNDAFHQADTHIFIIMGASGDLAKKKIYPTIWWLFRDGLLPKETFIVGY

Parental  ARSRLTVDDIRKQSEPFFKATPEERPKLEEFFARNSYVAGQYDDAASYKHLNSHMNALHQGMQANRLFYL
          ARS.LTVDDI.KQSEPFFKATPEERPKLEEFF.RNSYV.GQYDD.ASYKHLNS..NALHQGMQAN.LFYL
Retrocopy ARSQLTVDDIQKQSEPFFKATPEERPKLEEFFTRNSYVVGQYDDPASYKHLNSYINALHQGMQANHLFYL

Parental  ALPPTVYEAVTKNIQETCMSQTGWNRIIVEKPFGRDLQSSNQLSNHISSLFREDQIYRIDHYLGKEMVQN
          ALPPTVYEAVTKNIQETCMSQTG.NRIIVEKPFGRDLQSSNQLSNHISSLFREDQIYRIDHYL.KEMVQN
Retrocopy ALPPTVYEAVTKNIQETCMSQTGFNRIIVEKPFGRDLQSSNQLSNHISSLFREDQIYRIDHYLDKEMVQN

Parental  LMVLRFANRIFGPIWNRDNIACVILTFKEPFGTEGRGGYFDEFGIIRDVMQNHLLQMLCLVAMEKPATTG
          LMVLRFANRIFGPIWN.DNIACVILTFKEPFGTEGRGGYFDEFGIIRDVMQ.HLLQMLCLVAMEKPATT.
Retrocopy LMVLRFANRIFGPIWNGDNIACVILTFKEPFGTEGRGGYFDEFGIIRDVMQSHLLQMLCLVAMEKPATTD

Parental  SDDVRDEKVKVLKCISEVETDNVVLGQYVGNPNGEGEAANGYLDDPTVPHGSTTATFAAAVLYVENERWD
          SDDVR.EKVKVLK.ISEVETDNV.LGQYVGNPNGEGEAANGYLDDPTVP.GSTTATFAAAVLYV.NERWD
Retrocopy SDDVRNEKVKVLKRISEVETDNVILGQYVGNPNGEGEAANGYLDDPTVPRGSTTATFAAAVLYVKNERWD

Parental  GVPFILRCGKALNERKAEVRLQFRDVAGDIFHQQCKRNELVIRVQPNEAVYTKMMTKKPGMFFNPEESEL
          GVPFILRCGKALNERKAEVRLQFRD..GDIFHQ.CKRNELVIR.QPNEAVYT.MMTKKPGMFFNPEESEL
Retrocopy GVPFILRCGKALNERKAEVRLQFRDIPGDIFHQKCKRNELVIRMQPNEAVYTTMMTKKPGMFFNPEESEL

Parental  DLTYGNRYKNVKLPDAYERLILDVFCGSQMHFVRSDELREAWRIFTPLLHKIDREKPQPIPYVYGSRGPT
          DLTYGN.YKNVKLP.AYERLILDVFCG.QMHFVR.DELRE.WRIFTPLLHKI.REKPQP.PYVYGSRGPT
Retrocopy DLTYGNKYKNVKLPGAYERLILDVFCGCQMHFVRTDELREGWRIFTPLLHKIEREKPQPFPYVYGSRGPT

Parental  EADELMKRVGFQYEGTYKWVNPH
          EADELM.RVGFQY.GTYK....H
Retrocopy EADELMRRVGFQYKGTYKGTHKH

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	28.32 RPM
SRP007412_cerebellum	0.00 RPM	45.42 RPM
SRP007412_heart	0.06 RPM	6.85 RPM
SRP007412_kidney	0.00 RPM	29.51 RPM
SRP007412_liver	0.00 RPM	8.98 RPM
SRP007412_testis	35.31 RPM	7.73 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_174 was not detected

EST

1 EST(s) were mapped to retro_mmus_174 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CF105073	61809291	61809861	99.7	568	2	566

TSS

No TSS is located nearby retro_mmus_174 retrocopy 5' end.

Lab

retro_mmus_174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_174 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016775	2 retrocopies	retro_cjac_4026, retro_cjac_499,
Equus caballus	ENSECAG00000014994	1 retrocopy	retro_ecab_492,
Myotis lucifugus	ENSMLUG00000008210	1 retrocopy	retro_mluc_842,
Mus musculus	ENSMUSG00000031400	1 retrocopy	retro_mmus_174 ,
Sus scrofa	ENSSSCG00000025108	1 retrocopy	retro_sscr_818,