RetrogeneDB ID: retro_mmus_856

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:35772950..35774810(+)
• Located in intron of: None

Retrocopy information

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

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_856
ATGCCTGAGGAAGTGCACCATGGAGAGGAAGAGGTGGAGACCTTTGCCTCTCAGGCAGAAATTGTCCAGCTCATGTCCCT
CATCATCAATACTCTCTATTCAAACAAGGAATTTTCCTTCAGGAATTGATCTCTAATACTTCTGATACCCTGGACAAAAT
TCAGTATGAGAGCCTGACAGACCCTTCCAAGTTGGACAGAGGCAAAGAGCTGAAAATTGACATCATCCCCAACCCTCAGG
AGCATACGCTGACTTTGGTGGACATCGGCATTGGCATGACCAAGGCTGACCTCATTAATAACTTGGGAACCATTGCTAAG
TCTGGCACAAAGGCATTCATGGAGGCTCTTCAGGCTGGTGCAGATACCTCCATGATTGGGCAGTTTGGTGTCAGATTCTT
CTTGGCCTATCTAGTGGCAGAGAAAGTGGTTGTGATCACGAAGCACAATGATGATGAGCAGTATGCCTGGGAGTCTTCTG
CGGGTGGATCCTTCAACGCCCATGCAGATCATGGTGAGTCCATTGTCTGGGGTACCAAAGTGATCCTTCACCTCAAAGAA
GACCTGGCAGAGTACTTAGAGGTGAGGGAGGTCAAGGAAGTTGTGAAGAAACACTCCCAGATCATAGGCTATCCCAGCAT
CCTCTACTTGGAGAAGGAACAAGAGAAGGAGATCAGTGATGATGAGGCAGAGAAAGAGAAAGGTGAGAAAGGAGAAAGAT
AAGGTTAATGAGAAGAAGCCTAAGATTGAAGATGTGGGATCTGATGAGGAGAATGACAGCACAAAGATAAGAAAAAGAAA
ACAAAGAAGACCAAGGAGAAGTACATTGACCAGGAAGAGCTGAATAAGATGAAGCCTATCTGGACCAGAAATCCAGATGA
GCTCACTCAAGAGGAATATGGTAAATTCTATAAGAGCCTCACCAATAATTGGGAAGACCTCTTGGCAGTCAAGGACTTCT
CTGTAGATGGTCAGTTGAAATTCAGGGCATTGCTCTTCATTCCCCAGTGAGCTCCCCTTGGCCTTTTTGAAACAAGAAGA
ACAACAACAAATTCTATGTCCATTGTTCTTTCAGCATGGACAGCTTTGATGAGATGATACCTGAGTACCTCAACTTTATC
TGCAGTGCAGTTGACTCCAAGGACCTGTCCCTGAACATCTCCCGAGAAATGTTCCACCAGAGCAAGATCCTGAAAGTCAT
CTGCAAAAACATCGTGAAGAAGTGCCCCGAGCTCTTCTCTGAGTTGGCTGAAGACGAAGAGAACTACAAGAAGTTTTGTG
AAGCATTCTCCAAGAATTTGAAGCTTGGAATCCACATGGATTCCACTAACTATTTCCACCTCTCTGAGTCCCATTGCTTT
CACACCTCTCAGTCTGGAGATGAGATGACTTCCCTGTTAGAATATGTGTCTCACATGAAGGAGACACAGAAGTCCATCTA
CTATACCACTGGTGAAAACAAAGAGCAAGTGGCCAACTCTGCCTTTGTGGAGAGTGAGTGGAAACAGGGCTTTGAGGTAG
TGTACATAACTGAGCCTATTGATGAGTGCTCTGTACAGCAGCTCAAGGAATTTGATGGAAAGAGCCTGGTCTCAGTGACT
AAGGAAGGCCTAGAGCCACCAGAGGATGAGGAAAAGAAGAAGAAAATGGAGGAGAGCAAGGCAAAATTTGAGGATCACTG
TAGGCTATGAAGGAGATCTTAGACAAGAAGGTTGAAAAATTGACAATTTCCAATAAGCTTTTGTCTTCCCCCTGCTGCAT
TGTGACAAGCACTTAAGTCTGGACAGTCAGCATAGAATGCATCATGAAGTCCCAGGTACTGTGAGACAGTTCTACAATGG
GCTACATGATGGCCAAAAAG

Alignment

ORF - retro_mmus_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.76 %
• Parental protein coverage: 86.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKE-IFLRELISNASDALDKIRYESLTDPSKLDSGK
          MPEEVHHGEEEVETFA.QAEI.QLMSLIINT.YSNKE.IFL.ELISN.SD.LDKI.YESLTDPSKLD.GK
Retrocopy MPEEVHHGEEEVETFASQAEIVQLMSLIINTLYSNKE<IFLQELISNTSDTLDKIQYESLTDPSKLDRGK

Parental  ELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLV
          ELKIDIIPNPQE.TLTLVD.GIGMTKADLINNLGTIAKSGTKAFMEALQAGAD.SMIGQFGV.F..AYLV
Retrocopy ELKIDIIPNPQEHTLTLVDIGIGMTKADLINNLGTIAKSGTKAFMEALQAGADTSMIGQFGVRFFLAYLV

Parental  AEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFI
          AEKVVVITKHNDDEQYAWESSAGGSF...ADHGE.I..GTKVILHLKED..EYLE.R.VKEVVKKHSQ.I
Retrocopy AEKVVVITKHNDDEQYAWESSAGGSFNAHADHGESIVWGTKVILHLKEDLAEYLEVREVKEVVKKHSQII

Parental  GYPITLYLEKEREKEISDDEAEEE-KGEKEEEDKEDEEKPKIEDVGSDEEDDSGK-DKKKKTKKIKEKYI
          GYP..LYLEKE.EKEIS.D...E.......E.DK..E.KPKIEDVGSDEE.DS.K.DKKKKTKK.KEKYI
Retrocopy GYPSILYLEKEQEKEIS-DDEAEK>RKVRKEKDKVNEKKPKIEDVGSDEENDSTK<DKKKKTKKTKEKYI

Parental  DQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFE-N
          DQEELNK.KPIWTRNPD..TQEEYG.FYKSLTN.WED.LAVK.FSV.GQL.FRALLFIP..AP..LFE.N
Retrocopy DQEELNKMKPIWTRNPDELTQEEYGKFYKSLTNNWEDLLAVKDFSVDGQLKFRALLFIPQ*APLGLFE<N

Parental  KKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELF
          KK..NN.K.YV...F.MDS.DE.IPEYLNFI...VDS.DL.LNISREM..QSKILKVI.KNIVKKC.ELF
Retrocopy KK--NNNKFYVHCSFSMDSFDEMIPEYLNFICSAVDSKDLSLNISREMFHQSKILKVICKNIVKKCPELF

Parental  SELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYI
          SELAED.ENYKKF.EAFSKNLKLGIH.DSTN...LSE....HTSQSGDEMTSL.EYVS.MKETQKSIYY.
Retrocopy SELAEDEENYKKFCEAFSKNLKLGIHMDSTNYFHLSESHCFHTSQSGDEMTSLLEYVSHMKETQKSIYYT

Parental  TGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEES
          TGE.KEQVANSAFVE...K.GFEVVY.TEPIDE..VQQLKEFDGKSLVSVTKEGLE.PEDEE.KKKMEES
Retrocopy TGENKEQVANSAFVESEWKQGFEVVYITEPIDECSVQQLKEFDGKSLVSVTKEGLEPPEDEEKKKKMEES

Parental  KAKFENLCKL-MKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKK
          KAKFE..C.L.MKEILDKKVEK.TISN.L.SSPCCIVTST..WT...E.IMK.Q.L.D.STMGYMMAKK
Retrocopy KAKFEDHCRL<MKEILDKKVEKLTISNKLLSSPCCIVTST*VWTVSIECIMKSQVL*DSSTMGYMMAKK

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	1372.48 RPM
SRP007412_cerebellum	0.04 RPM	1586.48 RPM
SRP007412_heart	0.06 RPM	1520.80 RPM
SRP007412_kidney	0.06 RPM	1889.41 RPM
SRP007412_liver	0.05 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_856 was not detected

EST

No EST(s) were mapped for retro_mmus_856 retrocopy.

TSS

No TSS is located nearby retro_mmus_856 retrocopy 5' end.

Lab

retro_mmus_856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_856 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,