RetrogeneDB ID: retro_mmus_484

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:129796610..129797968(-)
• Located in intron of: ENSMUSG00000042581

Retrocopy information

• Ensembl ID: ENSMUSG00000089648
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nup54
• Ensembl ID: ENSMUSG00000034826
• Aliases: Nup54, 3110079L04Rik, 54kDa
• Description: nucleoporin 54 [Source:MGI Symbol;Acc:MGI:1920460]

Sequence

>retro_mmus_484
GGCACTCAGAACAAAGGTTTTGGCTTTGGTACTGGCTTTGGCACAACGACAGGAACTGGCACTGGTTTAGGCACTGGTTT
GGGAACCGGACTTGGATTTGGAGGATTTAACAGCAACAGCAGCAGCAGCAGACTTCTTTAGGTGGTCTCTTCAGTCAGCC
TACCCAGGCTCCTGCACAGTCTACCCAGCTCATCAACACTGCTAGTGCACTTTCTGCTCCAACGCTACTGGGGGATGAGA
GAGACGCCATCTTGGCAGAGTGGAACCAGTTGCAGGCCTTCTGGGGAACAGGAAAAGGATATTTCAATAATAACATTCCT
CCAGTGGAGTTTACCCAGGAGAATCCCTTTTGCCGGTTTAAGCCTGTAGGCTATAGTTGTATGCCCAATAATAAAGATGA
AGATGGGCTAGTAGTTTTAATTTTCAACAGAAAAGAAACAGATATTAGAAGCCAGCAACAGTAATTGGTACAATCATTGC
ATAAAGTTTTGGGAGGAAACCAAACCCTTACGGTCAATGTGGAGGGCATTAAGACGTTGCCGGATGATCAGACAGAAGTT
GTCATTTATGTTGTTGAGCGTTCTCCAAATGGCACCTCGAGAAGAGTTCCAGCGACAACACTGTATGCCCACTTTGAGCA
AGCCAACATTAAAGCCTAACTGCAGCAGCTTGGGGTGACCCTTTCTATGACCAGGACAGAACTGTCTCCCGCTCAGATCA
AGCAGCTCTTACAAAACCCTCCCGCAGGTGTTGATCCTATTATTTGGGAACAGGCCAAGGTGGATAACCCAGACTCTGAA
AAGTTAATTCCTGTACCAATGGTGGGTTTCAAAGAATTGCTTCGAAGACTGAAGGTTCAAGATCAGATGACTAAGCAGCA
TCAGACCAGACTAGATATCATATCTGAAGATATTAGTGAACTGCAAAAAAATCAAACTACAACTATGGCCAAAATAGCAC
AATACAAGAGGAAACTGATGGAGTTCTCCCACAGGACCTTACAGGTCCTAATCAAACAGGAAATCCAGAGGAAGAGTGGC
TATGCGATCCAGGCTGATGAAGAGCAGTTGCAGGTTCAGCTAGATATTATTCAAGGGGAACTGAATGCACCCACTCAGTT
CAAAGGTCGGCTGAATGAGCTGATGTCCCAGATCAGGATGCAGAATCATTTTGGAGCCGTGAAATCTGAAGAAAAGTACT
ACATAGATGCAGACCTATTACAAGAAATCAAGCAGCATTTGAAACAACAGGAAGGCCTTAGCCACTTGATTAGCATCATA
AAAGATGACCTAGAAGACATAAAACTGGTAGAACATGGATTGAATGAGACCATCCATAGCAGAGGCGGTGTCTTTAGC

Alignment

ORF - retro_mmus_484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.72 %
• Parental protein coverage: 89.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTQNKGFGFGTGFGTTTGTGTGLGTGLGTGLGFGGFNT-QQQQQQQQTSLGGLFSQPTQAPAQSTQLINT
          GTQNKGFGFGTGFGTTTGTGTGLGTGLGTGLGFGGFN..QQ..QQQQTSLGGLFSQPTQAPAQSTQLINT
Retrocopy GTQNKGFGFGTGFGTTTGTGTGLGTGLGTGLGFGGFNS<QQ--QQQQTSLGGLFSQPTQAPAQSTQLINT

Parental  ASALSAPTLLGDERDAILAKWNQLQAFWGTGKGYFNNNIPPVEFTQENPFCRFKAVGYSCMPNNKDEDGL
          ASALSAPTLLGDERDAILA.WNQLQAFWGTGKGYFNNNIPPVEFTQENPFCRFK.VGYSCMPNNKDEDGL
Retrocopy ASALSAPTLLGDERDAILAEWNQLQAFWGTGKGYFNNNIPPVEFTQENPFCRFKPVGYSCMPNNKDEDGL

Parental  VVLIFNKKETDIRSQQQQLVESLHKVLGGNQTLTVNVEGIKTLPDDQTEVVIYVVERSPNGTSRRVPATT
          VVLIFN.KETDIRSQQQ.LV.SLHKVLGGNQTLTVNVEGIKTLPDDQTEVVIYVVERSPNGTSRRVPATT
Retrocopy VVLIFNRKETDIRSQQQ*LVQSLHKVLGGNQTLTVNVEGIKTLPDDQTEVVIYVVERSPNGTSRRVPATT

Parental  LYAHFEQANIKAQLQQLGVTLSMTRTELSPAQIKQLLQNPPAGVDPIIWEQAKVDNPDSEKLIPVPMVGF
          LYAHFEQANIKA.LQQLGVTLSMTRTELSPAQIKQLLQNPPAGVDPIIWEQAKVDNPDSEKLIPVPMVGF
Retrocopy LYAHFEQANIKA*LQQLGVTLSMTRTELSPAQIKQLLQNPPAGVDPIIWEQAKVDNPDSEKLIPVPMVGF

Parental  KELLRRLKVQDQMTKQHQTRLDIISEDISELQKNQTTTMAKIAQYKRKLMELSHRTLQVLIKQEIQRKSG
          KELLRRLKVQDQMTKQHQTRLDIISEDISELQKNQTTTMAKIAQYKRKLME.SHRTLQVLIKQEIQRKSG
Retrocopy KELLRRLKVQDQMTKQHQTRLDIISEDISELQKNQTTTMAKIAQYKRKLMEFSHRTLQVLIKQEIQRKSG

Parental  YAIQADEEQLRVQLDTIQGELNAPTQFKGRLNELMSQIRMQNHFGAVKSEEKYYIDADLLREIKQHLKQQ
          YAIQADEEQL.VQLD.IQGELNAPTQFKGRLNELMSQIRMQNHFGAVKSEEKYYIDADLL.EIKQHLK.Q
Retrocopy YAIQADEEQLQVQLDIIQGELNAPTQFKGRLNELMSQIRMQNHFGAVKSEEKYYIDADLLQEIKQHLK-Q

Parental  QEGLSHLISIIKDDLEDIKLVEHGLNETIHSRGGVFS
          QEGLSHLISIIKDDLEDIKLVEHGLNETIHSRGGVFS
Retrocopy QEGLSHLISIIKDDLEDIKLVEHGLNETIHSRGGVFS

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	0.02 RPM	10.30 RPM
SRP007412_cerebellum	0.00 RPM	11.07 RPM
SRP007412_heart	0.00 RPM	9.49 RPM
SRP007412_kidney	0.08 RPM	14.65 RPM
SRP007412_liver	0.00 RPM	13.95 RPM
SRP007412_testis	0.09 RPM	11.48 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_484 was not detected

EST

No EST(s) were mapped for retro_mmus_484 retrocopy.

TSS

No TSS is located nearby retro_mmus_484 retrocopy 5' end.

Lab

retro_mmus_484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_484 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000001341	1 retrocopy	retro_dord_86,
Myotis lucifugus	ENSMLUG00000005318	1 retrocopy	retro_mluc_1042,
Mus musculus	ENSMUSG00000034826	1 retrocopy	retro_mmus_484 ,