RetrogeneDB ID: retro_mmus_1491

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:14038160..14038859(-)
• Located in intron of: ENSMUSG00000044117

Retrocopy information

• Ensembl ID: ENSMUSG00000082277
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hmgn5
• Ensembl ID: ENSMUSG00000031245
• Aliases: Hmgn5, GARP45, NBP-45, Nsbp1
• Description: high-mobility group nucleosome binding domain 5 [Source:MGI Symbol;Acc:MGI:1355295]

Sequence

>retro_mmus_1491
ATGCCCAAAAGAAAGATTGCAGGTGATACAAGCCAGGAGCCAAAGAGAAGATCAGCCCGATTGTCTCCTATGCCTGTAAC
CTTTACACTGGAGTTGAAACATAAAAGAGCACCAACTTCAAGGAAAAACAAGACCACAAATGTCATGGAAGAAAACAAAG
ATGCAGGTACCATACCAATTCCTGAAACTGAGCCAGAAGATGTTAAAGAAGAATGCAACGTGGAAAATGCTGAAAATGGA
GAAGCCAAGATTATTGAGGCACCCATTCCTAAAATGGAAGCTGAGGAAGTAAAGGAACATGTAAATGAAGACACTGAAGA
AGATGGAGGAGAAAAGAAGGAAGCAGTGGCAGCAGAAGACAAAGACGATAAGCTAGAAGCAAACATTCAAGATGTAGAGA
AAGATGAAGATGGAAAAGAGCACGAAGATACAGGTGAGGAGGTGGAAGGTGGAAAAAATGGAAGAAGAGGCCTAAAAGAG
AAACCAGGTGCAGCTGAAAGCAAAGATGCAAAGGATGCCAAAGATGATGAAGAGAAAGGAGACAGTGAAAAAGGAGAAGA
TGGCAGAGAGGAAGGCGATGGGAAGAAGGAAGAAGAGAAAGATCACAAAGAGGGGGACTCTGAAACAGAGGAAGAAGTAA
AAGAACAGAAGAAAGAAACTGAGGAGGAGGATGGGAAGTGCAAAGAGGAGGAAATCAAA

Alignment

ORF - retro_mmus_1491 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.69 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRKAAGDVSQEPKRRSARLSAMPVPFTPELKPKRASTSRKTKTTNVVEENKDASTIPIPETKPEDVKD
          MPKRK.AGD.SQEPKRRSARLS.MPV.FT.ELK.KRA.TSRK.KTTNV.EENKDA.TIPIPET.PEDVK.
Retrocopy MPKRKIAGDTSQEPKRRSARLSPMPVTFTLELKHKRAPTSRKNKTTNVMEENKDAGTIPIPETEPEDVKE

Parental  ECNMENAENGEAKIMEAPIPKMEAEEVKEQINEDTEEDGGEKKEAVAAEAKDDELKANIQDVEKDEDGKE
          ECN.ENAENGEAKI.EAPIPKMEAEEVKE..NEDTEEDGGEKKEAVAAE.KDD.L.ANIQDVEKDEDGKE
Retrocopy ECNVENAENGEAKIIEAPIPKMEAEEVKEHVNEDTEEDGGEKKEAVAAEDKDDKLEANIQDVEKDEDGKE

Parental  HKDTGEEVEDGKIEEEGLNEKPGTAKSEDAEVSKDEEEKGDNEKGEDGKEEGD-EKEEEKDDKEGDTGTE
          H.DTGEEVE.GK....GL.EKPG.A.S.DA...KD.EEKGD.EKGEDG.EEGD..KEEEKD.KEGD..TE
Retrocopy HEDTGEEVEGGKNGRRGLKEKPGAAESKDAKDAKDDEEKGDSEKGEDGREEGDGKKEEEKDHKEGDSETE

Parental  KEVKEQNKEAEEDDGKCKEEENK
          .EVKEQ.KE.EE.DGKCKEEE.K
Retrocopy EEVKEQKKETEEEDGKCKEEEIK

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	0.07 RPM	8.36 RPM
SRP007412_cerebellum	0.22 RPM	19.41 RPM
SRP007412_heart	0.00 RPM	21.23 RPM
SRP007412_kidney	0.02 RPM	51.86 RPM
SRP007412_liver	0.03 RPM	61.23 RPM
SRP007412_testis	0.09 RPM	19.03 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1491 was not detected

EST

No EST(s) were mapped for retro_mmus_1491 retrocopy.

TSS

No TSS is located nearby retro_mmus_1491 retrocopy 5' end.

Lab

retro_mmus_1491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1491 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000031245	1 retrocopy	retro_mmus_1491 ,