RetrogeneDB ID: retro_hsap_1530

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:99798149..99799982(+)
• Located in intron of: ENSG00000168904

Retrocopy information

• Ensembl ID: ENSG00000259706
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSP90B1
• Ensembl ID: ENSG00000166598
• Aliases: HSP90B1, ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1
• Description: heat shock protein 90kDa beta (Grp94), member 1 [Source:HGNC Symbol;Acc:12028]

Sequence

>retro_hsap_1530
TCTGACGCTTTAGTTAAGATAAGGCTGATATCACTGACTAATGAAAATGCTCTTTCTGGAAATGAGGAACTAACAGTCAA
AATTAAGTGTGATAAGGTGAAGAACCTACTGCATGTCACAGACACTGGTGTAGGAATGACCAGAGAAGAGTTGGTTAAAA
ACCTTGGTACCATAGCCAAATCTTGAACAAACGAGTTTTTAAACAAAATGACTGAAGCACAGGAAGATGGCCAGTCAACT
TCTGAATTGATTGGCCAGTTTGGTGTCAGTTTCTATTCCATCTTCCTTGTAGCAGATAAGGTTATTGTCACTTCAAAACA
CAACAACGATACCCAGTACATCTGGGAGTCTGAATCCAATGAATATTCTGTAATTGCTGACCCAAGAGGAAACACTCTAG
GACGGGGAACGACCATTACCCTTGTCTTAAAAGAAAAAGCATTTGATTACCTTGCATTGGATACAATTAAAAATCTCATC
AAAAATATTCACAGTTCATAAACTTTCCTATTTATGTATGGAGCAGCAAGACTGAAACTGTTAAGGAGCCATGAAGGAAG
AAGCAGCAGCAAAAGAAGAGAAAGAAGAATCTTATGATGAAGCTGCAGTAGAGGAAGAAGAAGAAAAACAGAAACCAAAG
ACTAAAAAAGTTGAAAAAACTGTCTGTGAATGGGAACTTATGAATGATATCAAACCAATATGGCAGAGACCATCCAAGAA
GTAGAAGATGAATACAAAGCTTTCTGCAAATCATTTTCAAAGGAAAGTGATGACCCTGTGGCTTGTATTCACTTTACTGC
TGAAGGAGAAGTTACCTTCAAATCAATTTTATTTGTACCCACATTTGTTCCACGTGGCCTATTTGATGAATATGGATCTA
AAAAGAGCGATTACATTAAGCTCTATGTGCGCTGTGTATTCATCACAGATGACTTCCGTGATACGATGCCTAAGAACCTG
AATTTTGTCAAGGGTGTGGTGGACTCAGGTGGTCTGTCTTTGAATGTTTCCTGTGAGACTCTTCAGCAACATAAACTGCT
TAAGGTGATTAGGAAGAAACTTGTTCATAAAACTCTGGACATGATCAAGAAGATTGCTGATGAGAAATACAATGATACTT
TTTGGAAAGAATTTGGTACCAACATTAAGCTTGGTGTAATTGAAGACCACTCGAATCGAACATGTCTTGCTAAACTTCTT
AGGTTCCAGTCTTCTCATCATCCAGCTGACATTACTAGCCTACACCAGGATGTTGAAAGAATGAAGGAAAAACAAGACAA
AATCTGCCTCATGGCTGGGTCCAGCAGAAAAGAGGCTGAATCTTCTCCATTTGTTTAGCGACTTCTGAAAAGGGGCTATG
AAGTTATTTACCTCACAGAACCTGTGGTTGAATACTGCATTCAGGCCCTTCCCGAATTTGATGGGAAGAGGTTCCAGAAT
GTTGCCAAGGAAGGAGTGAAGTTTGATGACAGTGAGAAAACTAAGGAGAGTCATGAAGCAGTTGAGAAAGAATTTGAGCC
TCTGCCCAATTGGGTGAAAGATAAAGCCATTAAGGACAAGATTGAAAAGGCTATGGTATCTCAGTGCCTGACAGAATCTC
TGTGTGCTTTGGTGGCCAGCCAGTACGGGTGGTCTGGCAACATGGAGAGAATCATGAAAGCACAAGCGTACCAAACGGGC
AAGGGCATCTCTACAAATTACCATGCGAGTCGGAAGAAAACATTTGAAATTAATCCCAGACATCCGCTGATCAGAGACAT
GCTTCGACGAATTAAGGAAGATGAAGATGATAAAACAGTTTTGGATCTTGCTGTGGTTTTGTTTGAAACAGCA

Alignment

ORF - retro_hsap_1530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.31 %
• Parental protein coverage: 76.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SDALDKIRLISLTDENALSGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKM
          SDAL.KIRLISLT.ENALSGNEELTVKIKCDK.KNLLHVTDTGVGMTREELVKNLGTIAKS.T.EFLNKM
Retrocopy SDALVKIRLISLTNENALSGNEELTVKIKCDKVKNLLHVTDTGVGMTREELVKNLGTIAKS*TNEFLNKM

Parental  TEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTIT
          TEAQEDGQSTSELIGQFGV.FYS.FLVADKVIVTSKHNNDTQ.IWES.SNE.SVIADPRGNTLGRGTTIT
Retrocopy TEAQEDGQSTSELIGQFGVSFYSIFLVADKVIVTSKHNNDTQYIWESESNEYSVIADPRGNTLGRGTTIT

Parental  LVLKEEASDYLELDTIKNLVK-KYSQFINFPIYVWSSKTETVEEP-MEEEEAAKEEKEESDDEAAVEEEE
          LVLKE.A.DYL.LDTIKNL.K.KYSQFINFPIYVWSSKTETV.EP.M.EE.AAKEEKEES.DEAAVEEEE
Retrocopy LVLKEKAFDYLALDTIKNLIK<KYSQFINFPIYVWSSKTETVKEP<MKEEAAAKEEKEESYDEAAVEEEE

Parental  EEKKPKTKKVEKTVWDWELMNDIKPIWQRPSK-EVEEDEYKAFYKSFSKESDDPMAYIHFTAEGEVTFKS
          .............V..WELMNDIKPIWQRPSK.EVE.DEYKAF.KSFSKESDDP.A.IHFTAEGEVTFKS
Retrocopy XXXXXXXXXXXXXVCEWELMNDIKPIWQRPSK<EVE-DEYKAFCKSFSKESDDPVACIHFTAEGEVTFKS

Parental  ILFVPTSAPRGLFDEYGSKKSDYIKLYVRRVFITDDFHDMMPKYLNFVKGVVDSDDLPLNVSRETLQQHK
          ILFVPT..PRGLFDEYGSKKSDYIKLYVR.VFITDDF.D.MPK.LNFVKGVVDS..L.LNVS.ETLQQHK
Retrocopy ILFVPTFVPRGLFDEYGSKKSDYIKLYVRCVFITDDFRDTMPKNLNFVKGVVDSGGLSLNVSCETLQQHK

Parental  LLKVIRKKLVRKTLDMIKKIADDKYNDTFWKEFGTNIKLGVIEDHSNRTRLAKLLRFQSSHHPTDITSLD
          LLKVIRKKLV.KTLDMIKKIAD.KYNDTFWKEFGTNIKLGVIEDHSNRT.LAKLLRFQSSHHP.DITSL.
Retrocopy LLKVIRKKLVHKTLDMIKKIADEKYNDTFWKEFGTNIKLGVIEDHSNRTCLAKLLRFQSSHHPADITSLH

Parental  QYVERMKEKQDKIYFMAGSSRKEAESSPFVERLLKKGYEVIYLTEPVDEYCIQALPEFDGKRFQNVAKEG
          Q.VERMKEKQDKI..MAGSSRKEAESSPFV.RLLK.GYEVIYLTEPV.EYCIQALPEFDGKRFQNVAKEG
Retrocopy QDVERMKEKQDKICLMAGSSRKEAESSPFV*RLLKRGYEVIYLTEPVVEYCIQALPEFDGKRFQNVAKEG

Parental  VKFDESEKTKESREAVEKEFEPLLNWMKDKALKDKIEKAVVSQRLTESPCALVASQYGWSGNMERIMKAQ
          VKFD.SEKTKES.EAVEKEFEPL.NW.KDKA.KDKIEKA.VSQ.LTES.CALVASQYGWSGNMERIMKAQ
Retrocopy VKFDDSEKTKESHEAVEKEFEPLPNWVKDKAIKDKIEKAMVSQCLTESLCALVASQYGWSGNMERIMKAQ

Parental  AYQTGKDISTNYYASQKKTFEINPRHPLIRDMLRRIKEDEDDKTVLDLAVVLFETA
          AYQTGK.ISTNY.AS.KKTFEINPRHPLIRDMLRRIKEDEDDKTVLDLAVVLFETA
Retrocopy AYQTGKGISTNYHASRKKTFEINPRHPLIRDMLRRIKEDEDDKTVLDLAVVLFETA

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
bodymap2_adipose	0.10 RPM	462.78 RPM
bodymap2_adrenal	0.12 RPM	1061.01 RPM
bodymap2_brain	0.47 RPM	312.46 RPM
bodymap2_breast	0.14 RPM	496.13 RPM
bodymap2_colon	0.14 RPM	1149.42 RPM
bodymap2_heart	0.24 RPM	292.66 RPM
bodymap2_kidney	0.48 RPM	1227.06 RPM
bodymap2_liver	1.12 RPM	1596.74 RPM
bodymap2_lung	0.23 RPM	865.24 RPM
bodymap2_lymph_node	0.42 RPM	1079.30 RPM
bodymap2_ovary	0.10 RPM	846.29 RPM
bodymap2_prostate	0.26 RPM	564.55 RPM
bodymap2_skeletal_muscle	0.27 RPM	114.75 RPM
bodymap2_testis	0.34 RPM	764.63 RPM
bodymap2_thyroid	0.53 RPM	2359.65 RPM
bodymap2_white_blood_cells	0.16 RPM	363.87 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1530 was not detected

EST

No EST(s) were mapped for retro_hsap_1530 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_48478	731 libraries	846 libraries	237 libraries	12 libraries	3 libraries
TSS #2	TSS_48479	328 libraries	377 libraries	934 libraries	154 libraries	36 libraries
TSS #3	TSS_48481	366 libraries	393 libraries	882 libraries	141 libraries	47 libraries

The graphical summary, for retro_hsap_1530 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 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_hsap_1530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Homo sapiens	ENSG00000096384	2 retrocopies	retro_hsap_2912, retro_hsap_2958,
Homo sapiens	ENSG00000166598	2 retrocopies	retro_hsap_1530 , retro_hsap_184,
Macaca mulatta	ENSMMUG00000023469	1 retrocopy	retro_mmul_391,
Nomascus leucogenys	ENSNLEG00000006510	1 retrocopy	retro_nleu_993,
Pan troglodytes	ENSPTRG00000005372	1 retrocopy	retro_ptro_170,