RetrogeneDB ID: retro_mmus_3624

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:60577233..60578379(-)
• Located in intron of: ENSMUSG00000062949

Retrocopy information

• Ensembl ID: ENSMUSG00000081729
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hspa9
• Ensembl ID: ENSMUSG00000024359
• Aliases: Hspa9, 74kDa, Csa, Grp75, Hsc74, Hsp74, Hsp74a, Hspa9a, Mortalin, Mot-2, Mot2, Mthsp70, Pbp74
• Description: heat shock protein 9 [Source:MGI Symbol;Acc:MGI:96245]

Sequence

>retro_mmus_3624
GCTGTAATCACAGTCTCTGCTTATTTCAATGATTCACAGTGACAGGCCACTAAGGATGCTGGTCAGATATCTGAGCTAAA
TGTGCTTTGAGTAATCAATGAGCCTACAGCTGCTGCTCTAGCTTAAGGTCTGGACAAATCTGAAGATAAAGTCATTGCTG
TGTATGATTTAGGTGGTGGAACCTTTGACATTTCTACCCTGGAGATTGAGAAAGGAGTGTTTGAGGTGAAATCTACCAAT
GGGGACCCTTTCTTAGGAGGGGAAGACTTTGACCAAGCTTTGTTACAGCACACTGTCAAGGAGTTCAAGAGAGAGACACG
GATGGATTTGACCAAAGACAACATGGCACTTCAGACGGTTTGGGAAGCTGCTGAGAAGGCGAAATGTGAACTTTCCTCAT
CTGTGCAAACTGACATCAACTTGCCATACCAAACCAAGGATGCTTCTGGACAAAAGCATTTGAATATGAAGCTGACTCGA
GCTCAGTTTGAAGGCCTTGTCACAGATCTAATCAAGGGAACTATTGCTCCGTGTCAGAAAGCTATGCAGGATGCAGAAGT
CAGCAAGAGTGACATAGAAGTGATTCTGGTTGGTGGCATGACAAGGACACCCAAGGTTCAGCAGACTGTACAAGATCTTT
TTGGCAGAGCCCCGAGTAAAGCTGTTAATCCTGATGAGGCTGTAGCCATCGGACCTCCCATTCAGGGAGGTGTTTTGGCT
GATGATGTTACAGATGTGCTACTCCTGGATGTCACTCCCCTCTCTCTGGGTATTGAGACTCTGGGAGGTGTCTTTACCAA
ACTTACTTACAGGAACACCAGTATTCCTACCAAAAAGAGCCAGGTGTTTTTTACTGCTGCTGATGGACAAACTCAAGTAG
AGGTTAAAGTGTGTCAGGGAGAACGAGAGATGGCTGAAGACAACAAACTTCTAGGACAGTTCACTTTGATTGGAATTCCC
CCAGCCCCTCGTGGAGTGCTCCAGACTGAAGTTACATTTGACATTGATGCCAATGGGATTGTGCACGTTTCTTCCAAAGA
TAACGGAACTGGTCGTGAGCAACAGATTGTAATCCAGTCTTCTGGTGGATTAAGCAAAGATGATATTGAAAATATAGTTT
AAAATGCAGAGAAATATGCTGAGGAG

Alignment

ORF - retro_mmus_3624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 56.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVITVPAYFNDSQRQATKDAGQISGLNVLRVINEPTAAALAYGLDKSEDKVIAVYDLGGGTFDISILEIQ
          AVITV.AYFNDSQ.QATKDAGQIS.LNVL.VINEPTAAALA.GLDKSEDKVIAVYDLGGGTFDIS.LEI.
Retrocopy AVITVSAYFNDSQ*QATKDAGQISELNVL*VINEPTAAALA*GLDKSEDKVIAVYDLGGGTFDISTLEIE

Parental  KGVFEVKSTNGDTFLGGEDFDQALLRHIVKEFKRETGVDLTKDNMALQRVREAAEKAKCELSSSVQTDIN
          KGVFEVKSTNGD.FLGGEDFDQALL.H.VKEFKRET..DLTKDNMALQ.V.EAAEKAKCELSSSVQTDIN
Retrocopy KGVFEVKSTNGDPFLGGEDFDQALLQHTVKEFKRETRMDLTKDNMALQTVWEAAEKAKCELSSSVQTDIN

Parental  LPYLTMDASGPKHLNMKLTRAQFEGIVTDLIKRTIAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQT
          LPY.T.DASG.KHLNMKLTRAQFEG.VTDLIK.TIAPCQKAMQDAEVSKSDI.EVILVGGMTR.PKVQQT
Retrocopy LPYQTKDASGQKHLNMKLTRAQFEGLVTDLIKGTIAPCQKAMQDAEVSKSDI-EVILVGGMTRTPKVQQT

Parental  VQDLFGRAPSKAVNPDEAVAIGAAIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKK
          VQDLFGRAPSKAVNPDEAVAIG..IQGGVLA.DVTDVLLLDVTPLSLGIETLGGVFTKL..RNT.IPTKK
Retrocopy VQDLFGRAPSKAVNPDEAVAIGPPIQGGVLADDVTDVLLLDVTPLSLGIETLGGVFTKLTYRNTSIPTKK

Parental  SQVFSTAADGQTQVEIKVCQGEREMAGDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGIVHVSAKDKG
          SQVF.TAADGQTQVE.KVCQGEREMA.DNKLLGQFTLIGIPPAPRGV.Q.EVTFDIDANGIVHVS.KD.G
Retrocopy SQVFFTAADGQTQVEVKVCQGEREMAEDNKLLGQFTLIGIPPAPRGVLQTEVTFDIDANGIVHVSSKDNG

Parental  TGREQQIVIQSSGGLSKDDIENMVKNAEKYAEE
          TGREQQIVIQSSGGLSKDDIEN.V.NAEKYAEE
Retrocopy TGREQQIVIQSSGGLSKDDIENIV*NAEKYAEE

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	0.05 RPM	209.61 RPM
SRP007412_cerebellum	0.00 RPM	231.48 RPM
SRP007412_heart	0.22 RPM	692.15 RPM
SRP007412_kidney	0.35 RPM	750.54 RPM
SRP007412_liver	0.05 RPM	600.49 RPM
SRP007412_testis	0.14 RPM	295.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3624 was not detected

EST

No EST(s) were mapped for retro_mmus_3624 retrocopy.

TSS

No TSS is located nearby retro_mmus_3624 retrocopy 5' end.

Lab

retro_mmus_3624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3624 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013579	2 retrocopies	retro_chof_2539, retro_chof_293,
Homo sapiens	ENSG00000113013	1 retrocopy	retro_hsap_2214,
Gorilla gorilla	ENSGGOG00000014154	1 retrocopy	retro_ggor_1747,
Mus musculus	ENSMUSG00000015656	8 retrocopies	retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Mus musculus	ENSMUSG00000024359	1 retrocopy	retro_mmus_3624 ,
Mus musculus	ENSMUSG00000026864	1 retrocopy	retro_mmus_1299,
Pan troglodytes	ENSPTRG00000017290	1 retrocopy	retro_ptro_1680,
Rattus norvegicus	ENSRNOG00000019525	1 retrocopy	retro_rnor_1797,