RetrogeneDB ID: retro_mmus_458

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:78783135..78784859(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hnrnpr
• Ensembl ID: ENSMUSG00000066037
• Aliases: Hnrnpr, 2610003J05Rik, 2610528B01Rik, Hnrpr
• Description: heterogeneous nuclear ribonucleoprotein R [Source:MGI Symbol;Acc:MGI:1891692]

Sequence

>retro_mmus_458
GGATTGGTAGCTTGTGTCGATCTTGATGAAAGAGCAACCGATGCTCTCAGGGAGTTTAATGAAGGAGCTCTGTCTGTACT
GCAGCAGTTCAAAGAAAGTGACCTGTCTCATGTCCAGAACAAAAGCGCATTTTATGTGGAGTTATGAAGACCTACAGGCA
AAGAGAGAAACAAGGCAGCAAGGTACAAGAGTCCACGAAAGGGCCCGATGAAGCAAAAAGCAAGGCCTTGCTTGAGAGGA
CTGGTTATACTTTGGATGTAACCACGGGACAGAGGAAGTATGGTGGTCCCCCACCAGACAGTACTCAGGTGTGCAACCTG
GAACTGGGACAGAGGTCTTCATAGGTAAAATCCCAAGAGACTTGTATGAGGATGAATTGGTGCCCCTTTTTGAGAAGGCT
GGTCCTATCTGGGATCTACGGCTCATGATGGATCCACTCTCTGGTCAGAACAGAGGCGATGCCTTTATCACCTTCTGTGG
AAAAGAAGCTGCTGAGGAAGCAGTTAAGCTGTGTGGCGGCTGTGAGATTCACCCTGGTAAACACCTGGGAGTGTGCATTT
CTGTGGCAAACAACAGACGTTTTGTTGGATCCATTCCAAAGAATAAAACTAAAGAGAACATTCTGGAAGAGTTCAGTAAA
GTCACAGAGGGTTTGGTGGGCGTTATTCTCTATCATCAACCCGATGACAAAAAGAAGAATCGGGGGTTCTGCTTCCTTGA
ATATGAGGACCACAAGTGAGCAGCACAAGCCAGACGCCGGCTGATGAGTGGAAAAGTCAAAGTGTGGGGAAATGTGGTTA
CAGTAGAGTGGGCTGACCCCGTGGAGGAGACGGATCCAGAAGTCATGGCAAAGGTAAAAGTTTTATTTGTGAGAAACTTG
GCAACTACGGTGACAGAAGAAATATTAGAGAAATCATTTTCTGAGTTTGGAAAACTGGAGAGAGTGAAGAAGTTGAAAGA
TTATGCGTTCGTTCACTTTGAGGACAGGGGAGCTGCTGTTAAGGCTATGGATGAAATGAATGGAAAAGAAATAGAAGGGG
AAGAAATTGAAATTGTCTTAGCTTAGCCACCAGACAAGAAAAGGAAAGAGCGCCAAGCTGCTAGACAGGCCTCCAGAAGC
ACTGCGTATGAAGATTATTATTATCACCCTCCTCCCCGAATGCCACCTCCAATGAGAGGCCAAGGTCGTGGAGGGAGAGG
TGGATATGGCTACCCTCCAGATTATTATGGTTATGAACACTACTATGATGATTACTATGGTTATGATTATCACGACTATC
GTGGAGGCTATAAAGATCCCTACTACAGCTATGATGATGGCTATGCAGTAAGAGGAGGAGGAAGGGGGGGCAAGGTGCTC
CACCACCACCAAGGGGGCGGGGAGACCACCTCCAAGAGGTAGAGCTGGCTATTCACAGAGGGGGGCACCTTTGGGACCAC
CAAGAGGCTCAAGGGGTGGCAGAGGGGGTCCTGCACAACAGCAGAGAGGCCGTGGTTCTCGTGGAGCTCGGGGCAATCGA
GGGGGCAATGTAGGAGGCAAGAGAAAGGCAGATGGGTACAACTAACCTGATTCCAAACGTCGTCAGACCAACAACCAACA
GAACTGGGGTTCCCAACCCATCGCTCAGCAGCCGCTTCAGCAAGGTGGTGACTATTCTGGTAACTATGGTTACAATAATG
ACAACCAAGAATTTTATCAGGATACTTATGGGCAACAGTGGAAA

Alignment

ORF - retro_mmus_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.18 %
• Parental protein coverage: 91.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GLVAYVDLDERAIDALREFNEEGALSVLQQFKESDLSHVQNKSAF-LCGVMKTYRQREKQGSKVQESTKG
          GLVA.VDLDERA.DALREFNE.GALSVLQQFKESDLSHVQNKSAF.LCGVMKTYRQREKQGSKVQESTKG
Retrocopy GLVACVDLDERATDALREFNE-GALSVLQQFKESDLSHVQNKSAF<LCGVMKTYRQREKQGSKVQESTKG

Parental  PDEAKIKALLERTGYTLDVTTGQRKYGGPPPDSV-YSGVQPGIGTEVFVGKIPRDLYEDELVPLFEKAGP
          PDEAK.KALLERTGYTLDVTTGQRKYGG.PP....YSGVQPG.GTEVF.GKIPRDLYEDELVPLFEKAGP
Retrocopy PDEAKSKALLERTGYTLDVTTGQRKYGG-PPPDS<YSGVQPGTGTEVFIGKIPRDLYEDELVPLFEKAGP

Parental  IWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLCDSYEIRPGKHLGVCISVANNRLFVGSIPKNKTKE
          IWDLRLMMDPLSGQNRG.AFITFCGKEAA.EAVKLC...EI.PGKHLGVCISVANNR.FVGSIPKNKTKE
Retrocopy IWDLRLMMDPLSGQNRGDAFITFCGKEAAEEAVKLCGGCEIHPGKHLGVCISVANNRRFVGSIPKNKTKE

Parental  NILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVVTVEWADPVE
          NILEEFSKVTEGLV.VILYHQPDDKKKNRGFCFLEYEDHK.AAQARRRLMSGKVKVWGNVVTVEWADPVE
Retrocopy NILEEFSKVTEGLVGVILYHQPDDKKKNRGFCFLEYEDHK*AAQARRRLMSGKVKVWGNVVTVEWADPVE

Parental  EPDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGKEIE
          E.DPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGKEIE
Retrocopy ETDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGKEIE

Parental  GEEIEIVLAKPPDKKRKERQAARQASRSTAYEDYYYHPPPRMPPPMRGRGRGGRGGYGYPPDYYGYEDYY
          GEEIEIVLA.PPDKKRKERQAARQASRSTAYEDYYYHPPPRMPPPMRG.GRGGRGGYGYPPDYYGYE.YY
Retrocopy GEEIEIVLA*PPDKKRKERQAARQASRSTAYEDYYYHPPPRMPPPMRGQGRGGRGGYGYPPDYYGYEHYY

Parental  DDYYGYDYHDYRGGYEDPYYGYDDGYAVRGRGGGRGGR-GAPPPPRGR-GAPPPRGRAGYSQRGAPLGPP
          DDYYGYDYHDYRGGY.DPYY.YDDGYAV..RGGGRGG..GAPPPPRGR.G.PPPRGRAGYSQRGAPLGPP
Retrocopy DDYYGYDYHDYRGGYKDPYYSYDDGYAV--RGGGRGGK<GAPPPPRGR<GRPPPRGRAGYSQRGAPLGPP

Parental  RGSRGGRGGPAQQQRGRGSRGARGNRGGNVGGKRKADGYNQPDSKRRQTNNQQNWGSQPIAQQPLQQGGD
          RGSRGGRGGPAQQQRGRGSRGARGNRGGNVGGKRKADGYN.PDSKRRQTNNQQNWGSQPIAQQPLQQGGD
Retrocopy RGSRGGRGGPAQQQRGRGSRGARGNRGGNVGGKRKADGYN*PDSKRRQTNNQQNWGSQPIAQQPLQQGGD

Parental  YSGNYGYNNDNQEFYQDTYGQQWK
          YSGNYGYNNDNQEFYQDTYGQQWK
Retrocopy YSGNYGYNNDNQEFYQDTYGQQWK

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	0.14 RPM	50.77 RPM
SRP007412_cerebellum	0.00 RPM	40.99 RPM
SRP007412_heart	0.06 RPM	28.42 RPM
SRP007412_kidney	0.10 RPM	34.76 RPM
SRP007412_liver	0.00 RPM	15.10 RPM
SRP007412_testis	0.09 RPM	49.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_458 was not detected

EST

No EST(s) were mapped for retro_mmus_458 retrocopy.

TSS

No TSS is located nearby retro_mmus_458 retrocopy 5' end.

Lab

retro_mmus_458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_458 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000125944	1 retrocopy	retro_hsap_651,
Gorilla gorilla	ENSGGOG00000013250	1 retrocopy	retro_ggor_568,
Macaca mulatta	ENSMMUG00000010970	1 retrocopy	retro_mmul_2433,
Monodelphis domestica	ENSMODG00000016144	1 retrocopy	retro_mdom_240,
Mus musculus	ENSMUSG00000044595	1 retrocopy	retro_mmus_2548,
Mus musculus	ENSMUSG00000066037	1 retrocopy	retro_mmus_458 ,
Otolemur garnettii	ENSOGAG00000009179	1 retrocopy	retro_ogar_3144,
Procavia capensis	ENSPCAG00000010462	1 retrocopy	retro_pcap_88,
Pan troglodytes	ENSPTRG00000000324	1 retrocopy	retro_ptro_474,
Tupaia belangeri	ENSTBEG00000002251	1 retrocopy	retro_tbel_4256,