RetrogeneDB ID: retro_mmus_2139

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:18009368..18010993(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082896
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hsp90aa1
• Ensembl ID: ENSMUSG00000021270
• Aliases: Hsp90aa1, 86kDa, 89kDa, AL024080, AL024147, Hsp86-1, Hsp89, Hsp90, Hspca, hsp4
• Description: heat shock protein 90, alpha (cytosolic), class A member 1 [Source:MGI Symbol;Acc:MGI:96250]

Sequence

>retro_mmus_2139
GAAAGAAGACCAAACTATTTGGAGGAAAGGAGAATAAAGGAGATCGTGAAGAAGCATTCTCACTTCATTGGCTATCCCAT
TACTCTCTTTGTGGAGAAGGAACGAGATAAGGAAGTCAGTGATGATGAGGCTGAAGAAAAGGAAGAGAAAGAGGAAGAGA
AAGAAAAAGAAGAAAAGGAGTCTGATGATAAACCTGAAATAGAAGATGTTGGCTCTGATGAAGAAGAGGAGGAGAAGAAG
GATGGTGGCAAGAAGAAAAAGAAGAAGATAAAGGAAAAGCACATTGATCAAGAAGAACTCAACAAAACAAAGCCGATTTG
GACGCGAAATCCTGATGACATCACTAATGAGGAATATGGAGAGTTCTACAAGAGCTTAACCAACGATTGGGAAGAACACT
TGGCAGTAAAGCATTTTTCTGTTGAAGGACAATTAGAATTCCGGGCCCTTCTTTTTGTCCCAAGACGCGCTCCTTTTGAT
CTGTTTGAAAACAGAAAGAAAAAGAACAACATCAAGTTGTATGTTCGCAGAGTTTTTATCATGGATAACTGTGAGGAGTT
AATCCCTGAGTATCTGAATTTCATTAGAGGGGTAGTGGATTCTGAGGATCTCCCTCTAAATATTTCCCATGAAAGGCTGC
AACAAAGTAAAATTCTGAAAGTTATCAGAAAGAATTTGGTCAAGAAATGCTTAGAACTATTTACTGAACTAGCAGAAGAT
AAAGAGAACTACAAAAAGTTTTATGAGCAGTTCTCAAAAAATATAAAGCTTGGAATTCACGAGGACTTTCAGAATCGGAA
GAAGCTTTCAGAGCTGTTGTGGTACTACACATCTGCTTCTGGGGATGAGATGGTTTCTCTGAAGGACTACTGCACCAGAA
TGAAGGAAAACCAGAAGCACATCTATTTTATCACAGGTGAGACCAAGGACCAGGTTGCTAACTCCGCCTTTGTGGAACGT
CTCCGAAGGCAGGCTTAGAAGTAATTTATATGATTGAGCCCATTGATGAGTATTGTGTGCAACAGCTGAAGGAATTTGAG
GGCAAGACCTTGGTGTCTGTTACCAAAGAAGGACTGGAACTTCCAGAAGATGAAGAGGAAAAGAAGAAATAGGAAGAGAA
AAAGACAAAATTTGAGAACCTCTGCAAAATTATGAAAGATATTTTGGAGAAGAAGGTTGAAAAGGTGGTTGTGTCAAACC
GACTGGTGACATCCCCGTGCTGTATTTTCACAAGCACATATGGGTGGACAGCAAACATGGAGAGAATCATGAAAGCTCAA
GCCCTCAGAGACAACTCAACAATGGGTTACAAGGCAGCAAAGAAACACCTGGAGATAAATCCTGATCACTCCTTTATTGA
AACCTTAAGGCAAAAGGCAGAGGCTGACAAGAATGACAAATCTGTGAAGGATCTGGTCATCTTGCTGTATGAAACTGCAC
TCCTATCTTCTGGCTTCAGTCTGGAAGATCCCCAGACCCATGCTAACAGGATCTACAGGATGATCAAGCTTGGTCTAGGT
ATTGATGAGGATGATCCTACTGTGGATGACACCAGTGCTGCTGTAACTGAAGAAATGCCTCCCCTGGAAGGAGATGACGA
CACATCACGCATGGAAGAAGTAGAC

Alignment

ORF - retro_mmus_2139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 73.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAEEKEEKEEEKEKEEKESDDKPEIEDV
          E....YLEERRIKEIVKKHS.FIGYPITLFVEKERDKEVSDDEA...............ESDDKPEIEDV
Retrocopy ERRPNYLEERRIKEIVKKHSHFIGYPITLFVEKERDKEVSDDEAXXXXXXXXXXXXXXXESDDKPEIEDV

Parental  GSDEEEEEKKDGDKKKKKKIKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEEHLAVKHFS
          GSDEEEE.................IDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEEHLAVKHFS
Retrocopy GSDEEEEXXXXXXXXXXXXXXXXHIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEEHLAVKHFS

Parental  VEGQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISR
          VEGQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNIS.
Retrocopy VEGQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISH

Parental  EMLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSAS
          E.LQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHED.QNRKKLSELL.YYTSAS
Retrocopy ERLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDFQNRKKLSELLWYYTSAS

Parental  GDEMVSLKDYCTRMKENQKHIYFITGETKDQVANSAFVERLR-KHGLEVIYMIEPIDEYCVQQLKEFEGK
          GDEMVSLKDYCTRMKENQKHIYFITGETKDQVANSAFVERLR.K.GLEVIYMIEPIDEYCVQQLKEFEGK
Retrocopy GDEMVSLKDYCTRMKENQKHIYFITGETKDQVANSAFVERLR<KAGLEVIYMIEPIDEYCVQQLKEFEGK

Parental  TLVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTAN
          TLVSVT....................TKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCI.TSTYGWTAN
Retrocopy TLVSVTXXXXXXXXXXXXXXXXXXXXTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIFTSTYGWTAN

Parental  MERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLE
          MERIMKAQALRDNSTMGY.AAKKHLEINPDHS.IETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLE
Retrocopy MERIMKAQALRDNSTMGYKAAKKHLEINPDHSFIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLE

Parental  DPQTHANRIYRMIKLGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSRMEEVD
          DPQTHANRIYRMIKLGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSRMEEVD
Retrocopy DPQTHANRIYRMIKLGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSRMEEVD

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	0.26 RPM	397.40 RPM
SRP007412_cerebellum	0.09 RPM	379.59 RPM
SRP007412_heart	0.06 RPM	59.83 RPM
SRP007412_kidney	0.19 RPM	233.75 RPM
SRP007412_liver	0.08 RPM	143.56 RPM
SRP007412_testis	0.50 RPM	686.95 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2139 was not detected

EST

No EST(s) were mapped for retro_mmus_2139 retrocopy.

TSS

No TSS is located nearby retro_mmus_2139 retrocopy 5' end.

Lab

retro_mmus_2139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2139 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139 ,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,