RetrogeneDB ID: retro_mmus_1916

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:50909777..50911134(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083270
• Aliases: Gm13498, OTTMUSG00000012426
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hsp90ab1
• Ensembl ID: ENSMUSG00000023944
• Aliases: Hsp90ab1, 90kDa, AL022974, C81438, Hsp84, Hsp84-1, Hsp90, Hspcb
• Description: heat shock protein 90 alpha (cytosolic), class B member 1 [Source:MGI Symbol;Acc:MGI:96247]

Sequence

>retro_mmus_1916
TATTCAAACAAGAAGATTTTCCTCCAGGAGTTGATCTCTAATGCTTCTGATGACCTGGACAAGATTCAGTATGATAGCCT
GATGGACCCTAGCAAGTTGAACAGCAGGAAAGAGCTGAAAATTGACAGTATCCCCAACCCTCAGGTTGCCACACTGACTT
TGGTGAACACAGGCATTGGCATGACCAAGACTGACCTCATTAATAACTTGAGAACCATTGCTAAGTCTGGCACAAAGGCG
TTCATGGAGGCTCTCCAGGCCGGTACAGACATCTCCATGACTGAGTAGCTTGGTGTAGGATTCTACTCAGCCTATCTAGT
GGCAGAGAAAGTGGTTGGGATCACAAAGCACAGCAGTGATGAGAAGTATGCCTGGGAGTCTTCTGTTGCTGGATCCTTCA
CTGTTCATGCAGACCATGGTGAGCCCATTGGATAGGGTACCAAAGTGATCCTTCACCTCAAAGAAGATCAGACAGAGTAC
TTAGAGGAGAGGAGGGTCAAGGAAGTGGTGAAGAAACACTTGCAGATCATAGGCTGTCCCATCACCCTGTACTTAGAGAA
GGAACAAGAGAAGGAGATCAGTGATGATGAGGCAGAGGAAAAGAAAGGTGAGAAAGATGAGGAAGATGAGGATGAGAAGA
AGCCAAAGATTAAAGATGTAGGATCTGATAAGGAAGATGACAATGACAAAGATAAGAAAAAGAAAACAAAGAAGATCAAG
AAGTATATTGGCCAAGAAGAGCTGAATAAGATGAAGCCTATCTGGACCAGAAATCCAGATGACATCACTCAAGAGGAGTA
TGGTGAATTCTATAAGAGCCTTATCAATTATTGGGAAGACTACTTGGCAGTCAAGTAGTTCTCTGAAAAAGGTCAGGTGG
AATTCAGGGCATTGCTCTTCATTCCCTGGTGAGCTCCCTTTGACCTTTTTGAGAACAACATAGAAGAATATCAACATCAA
ATTTTATGTCCGCCATGTTTTCATCATGGACAGCTGTGATGAGTTGATACCTGAGTCCCTCAATTTTATCCATGGTGTGG
TTGACTCCAAGGACCTGCCTCTGAACATCTCCCGAGAAATGCTCCAAAAGATCAAGATCCTGAAAGTCATACGCAAGAAC
ATTGTGAAGAAGTGCCTTGAGCTCTTCTCTGAGTTGATTGAAGATGAAGAAAACTACAGGAAGTTTTATGAGATATTCTC
CAAGAATTTGAAGCTTGGAATCCATTCGGATTCCACTAACCATTGCCGGCTCTCTGAGCTCCTTCGTGATCACACCTCTC
AGTCTGGAGATGAGATGACTTCTCTGTCAGAGTATGGGTATTGCATGAAGGAGACACAGAAGTCCATCTACTGTATC

Alignment

ORF - retro_mmus_1916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.32 %
• Parental protein coverage: 62.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNL
          YSNK.IFL.ELISNASD.LDKI.Y.SL.DPSKL.S.KELKID.IPNPQ..TLTLV.TGIGMTK.DLINNL
Retrocopy YSNKKIFLQELISNASDDLDKIQYDSLMDPSKLNSRKELKIDSIPNPQVATLTLVNTGIGMTKTDLINNL

Parental  GTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHG
          .TIAKSGTKAFMEALQAG.DISM....GVGFYSAYLVAEKVV.ITKH..DE.YAWESS..GSFTV.ADHG
Retrocopy RTIAKSGTKAFMEALQAGTDISMTE*LGVGFYSAYLVAEKVVGITKHSSDEKYAWESSVAGSFTVHADHG

Parental  EPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDK
          EPIG.GTKVILHLKEDQTEYLEERRVKEVVKKH.Q.IG.PITLYLEKE.EKEISDDEAEE..........
Retrocopy EPIG*GTKVILHLKEDQTEYLEERRVKEVVKKHLQIIGCPITLYLEKEQEKEISDDEAEEXXXXXXXXXX

Parental  EDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDW
          ....KPKI.DVGSD.EDD..KDKKKKTKKIK.KYI.QEELNK.KPIWTRNPDDITQEEYGEFYKSL.N.W
Retrocopy DE-KKPKIKDVGSDKEDDNDKDKKKKTKKIK-KYIGQEELNKMKPIWTRNPDDITQEEYGEFYKSLINYW

Parental  EDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKK-KKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVV
          ED.LAVK.FS..GQ.EFRALLFIP..APFDLFEN...K..NIK.YVR.VFIMDSCDELIPE.LNFI.GVV
Retrocopy EDYLAVK*FSEKGQVEFRALLFIPW*APFDLFENNI>KNINIKFYVRHVFIMDSCDELIPESLNFIHGVV

Parental  DSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRL
          DS.DLPLNISREMLQ..KILKVIRKNIVKKCLELFSEL.ED.ENY.KFYE.FSKNLKLGIH.DSTN..RL
Retrocopy DSKDLPLNISREMLQKIKILKVIRKNIVKKCLELFSELIEDEENYRKFYEIFSKNLKLGIHSDSTNHCRL

Parental  SELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYI
          SELLR.HTSQSGDEMTSLSEY...MKETQKSIY.I
Retrocopy SELLRDHTSQSGDEMTSLSEYGYCMKETQKSIYCI

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	1372.48 RPM
SRP007412_cerebellum	0.00 RPM	1586.48 RPM
SRP007412_heart	0.00 RPM	1520.80 RPM
SRP007412_kidney	0.04 RPM	1889.41 RPM
SRP007412_liver	0.00 RPM	1439.73 RPM
SRP007412_testis	0.00 RPM	375.01 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1916 was not detected

EST

No EST(s) were mapped for retro_mmus_1916 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_87441	397 libraries	542 libraries	131 libraries	2 libraries	0 libraries
TSS #2	TSS_87442	241 libraries	426 libraries	380 libraries	19 libraries	6 libraries

The graphical summary, for retro_mmus_1916 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1916 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
Gorilla gorilla	ENSGGOG00000008889	2 retrocopies	retro_ggor_1011, retro_ggor_701,
Macropus eugenii	ENSMEUG00000013735	1 retrocopy	retro_meug_1896,
Myotis lucifugus	ENSMLUG00000005239	2 retrocopies	retro_mluc_1604, retro_mluc_865,
Macaca mulatta	ENSMMUG00000022686	2 retrocopies	retro_mmul_1319, retro_mmul_1869,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916 , retro_mmus_3528, retro_mmus_856,
Otolemur garnettii	ENSOGAG00000011961	1 retrocopy	retro_ogar_2574,
Pongo abelii	ENSPPYG00000016655	2 retrocopies	retro_pabe_2425, retro_pabe_415,
Rattus norvegicus	ENSRNOG00000019834	6 retrocopies	retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tupaia belangeri	ENSTBEG00000014873	1 retrocopy	retro_tbel_1428,