RetrogeneDB ID: retro_hsap_2912

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:13338105..13340247(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000205940
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSP90AB1
• Ensembl ID: ENSG00000096384
• Aliases: HSP90AB1, D6S182, HSP84, HSP90B, HSPC2, HSPCB
• Description: heat shock protein 90kDa alpha (cytosolic), class B member 1 [Source:HGNC Symbol;Acc:5258]

Sequence

>retro_hsap_2912
ATGCCTGAGGAAGTGCACCTTGGAGAGAAGGAGGTGGAGACTTTTGCCTTTCAGGCAGAAATTGCCCAACTCATGTCTCT
TATCATCAATACCTTCTATTCCAACAAGGAGATTTTCCTTTGGGAGTTGATCTCTAATGCTTCTGATGCCTTGGACAAGA
TTCGCTATGAAAGCCTAACAGACCCTTCCAAGTTGGACAGTGGTAAAGAGCTGAAAATTGACATCATCCCCAATACTCAG
GAACATACCCTGACTTTGGTAGACACAGGCATTGGCATGACCAAAGCTGATCTCATAAATAATTTGGGAACCATTGCCAA
GTTTCGTACGAAAGCATTCATGGAGGCTTTTTAGGCTGGCGCAGACATCTCCATGATTGGGCAATTTGGTATTGGCTTTT
ATTCTGCCTACCTGGTAGCAGAGAAAGTGGTTGTGATCACAAAGCCCAATGATGATGGCATGCCTGAGAGTCTTCTGCTG
GAGGTTCCTTCACTGTGTGTGCTGACCATGGTGAGCCTATTGGTAGGGGTACCAAAGTGATCCTCCACCTTAAAGAAGAT
CAGACAGAGTACTTAGAAGAGATGCAGGTCAAAGAAGTAGTGGAGAAGCACTCTCAGTTCCTAGGCTATCCCATCACCCT
TTATCTGGAGAAGGAACGAGAGAAAGAAATTAGTGATGGTAAGGCAGAGGAAGAGAAAGGTGAGAAAGAAGAGGAAAATA
AAGATGACGAAGAAAAGCCCAAGATCGAAGATGTGGGTTCAGATGAGGAGGATGACAGTGGTAAGGATAAGAAGAAGAAA
ACTAAGAAGATCAAAGAGAAATACATTGATCAGGAAGAACTAAACAAGACCAAGCCTATTTGGACCAGAAACACTGAAGA
CATCACCCAAGAGGAGTATGGAGAATTCTATAAGAGCCTCACCAATGACTGGAAAGACCACTTGGCAGTCAGGTACTTTT
CTGTAGAAGGTCAGTTGGAATTCAGGGCATTGCTATTCATTCCTCCTTAGGCTCCCTTTCATCTTTTTGAGAACAAGAAG
AAAAAGAACAACATCAAACTCTATGTCCATCGTGTGTTCATCAGGGACAGCTGTGTTGAGTTGATACCAGAGTGTCTCAA
CTTTATCCGTGGTGTGGTTGACTCTGAGGATTTCCCCTGAACATCTCCTGAGAAATGCTCCAGCAGAGCAAAATCTTCAA
AGTCATTCACAGAAACATTGTTAAGAAGTGCCTTGAGCTCTTCACTGAGCTGGTGGAAGACAAGGAGAATTACAAGAAAT
TCTATGAGGCATTCTCTAAAAATCTCAAGCTTGGAATCCACAAGGACTCCACTAACTGATGCCACCCGTCTGAGCTGCTG
TGTTATCACACCTCCCAGTCTGGAGATGAGATGATATCTTTGTTAGAGTATGTTTCTCGCATGAAGGAGATACAGAAGTC
CATCTATTACATCACTGGTGAGAGCAAAGAGCAGGTTGCCAACTCAGCTTTTGTGGAGCAAGTATGGAAGCGGGACTCCA
GGGTGGTATATATGACCGAGCCCATTGATGGCTACGTGTGCAGCAACTCAAGGAGTTTGATGGGAAGAGCCTGGTCTCAG
TTACCAAGGAGGGCCTGGAGCTACCTGAGGATGGGGAGGAGAAGAAGAGAATGGAAGAGAGGAAGGCAAAGTTTGAGAAC
CTCTGCAAGTTCATGAAAGAAACTTTAGATAAGAAGGTTGAGATGGTGACAGTCTCCAACAGGCTTGTGTCTTCATCCTG
CTGCATTGTGACCAGCACCTACAGCTGGACAGCCAATATGGAGCAGATCATGAAAGCCTAGGCACTTCGGGTCACCTCCA
CCGTGGGCTATATGATGGCCAAAAAGCACCTGGAGATCAACCCCAACCACCCCATTGTGGAGACGCTGCGGCAGAAGGCT
GAGACACACAAGAATGACAAGGCAGTCAAGGACCTGGTGGTGCTGCCGTTAGAAACTGCCTTGCTGTCTTCTGGCTTTTC
CCTTGAGGATCCCCAGACCCATTCCAACCACATCTACTGCATGATCAAGCTAGGTCTAGGTATCGATGAAGATTAAGTGA
CAGCAGAGGAACACAGTGCTGTGGTTCCTGATGAGATCACCCCTCTTGAGGGTGACGAGGAT

Alignment

ORF - retro_hsap_2912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.7 %
• Parental protein coverage: 98.9 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKE
          MPEEVH.GE.EVETFAFQAEIAQLMSLIINTFYSNKEIFL.ELISNASDALDKIRYESLTDPSKLDSGKE
Retrocopy MPEEVHLGEKEVETFAFQAEIAQLMSLIINTFYSNKEIFLWELISNASDALDKIRYESLTDPSKLDSGKE

Parental  LKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVA
          LKIDIIPN.QE.TLTLVDTGIGMTKADLINNLGTIAK..TKAFMEA..AGADISMIGQFG.GFYSAYLVA
Retrocopy LKIDIIPNTQEHTLTLVDTGIGMTKADLINNLGTIAKFRTKAFMEAF*AGADISMIGQFGIGFYSAYLVA

Parental  EKVVVITKHNDDEQ-YAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFI
          EKV.V......D....A.ESSAGGSFTV.ADHGEPIGRGTKVILHLKEDQTEYLEE..VKEVV.KHSQF.
Retrocopy EKV-VVITKPNDDG<HA*ESSAGGSFTVCADHGEPIGRGTKVILHLKEDQTEYLEEMQVKEVVEKHSQFL

Parental  GYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQ
          GYPITLYLEKEREKEISD...................KPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQ
Retrocopy GYPITLYLEKEREKEISDGKXXXXXXXXXXXXXXXXXKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQ

Parental  EELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKK
          EELNKTKPIWTRN..DITQEEYGEFYKSLTNDW.DHLAV..FSVEGQLEFRALLFIP..APF.LFENKKK
Retrocopy EELNKTKPIWTRNTEDITQEEYGEFYKSLTNDWKDHLAVRYFSVEGQLEFRALLFIPP*APFHLFENKKK

Parental  KNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSED-LPLNISREMLQQSKILKVIRKNIVKKCLELFSE
          KNNIKLYV.RVFI.DSC.ELIPE.LNFIRGVVDSED..PLNIS.EMLQQSKI.KVI..NIVKKCLELF.E
Retrocopy KNNIKLYVHRVFIRDSCVELIPECLNFIRGVVDSED<FPLNIS*EMLQQSKIFKVIHRNIVKKCLELFTE

Parental  LAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITG
          L.EDKENYKKFYEAFSKNLKLGIH.DSTN....SELL.YHTSQSGDEM.SL.EYVSRMKE.QKSIYYITG
Retrocopy LVEDKENYKKFYEAFSKNLKLGIHKDSTN*CHPSELLCYHTSQSGDEMISLLEYVSRMKEIQKSIYYITG

Parental  ESKEQVANSAFVERVRKRGFEVVYMTEPIDEYC-VQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESK
          ESKEQVANSAFVE.V.KR...VVYMTEPID.Y..VQQLKEFDGKSLVSVTKEGLELPED.EEKK.MEE.K
Retrocopy ESKEQVANSAFVEQVWKRDSRVVYMTEPIDGYV<VQQLKEFDGKSLVSVTKEGLELPEDGEEKKRMEERK

Parental  AKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLE
          AKFENLCK.MKE.LDKKVE.VT.SNRLVSS.CCIVTSTY.WTANME.IMKA.ALR..ST.GYMMAKKHLE
Retrocopy AKFENLCKFMKETLDKKVEMVTVSNRLVSSSCCIVTSTYSWTANMEQIMKA*ALRVTSTVGYMMAKKHLE

Parental  INPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAA
          INP.HPIVETLRQKAE..KNDKAVKDLVVL..ETALLSSGFSLEDPQTHSN.IY.MIKLGLGIDED.V.A
Retrocopy INPNHPIVETLRQKAETHKNDKAVKDLVVLPLETALLSSGFSLEDPQTHSNHIYCMIKLGLGIDED*VTA

Parental  EEPNAAVPDEIPPLEGDED
          EE..A.VPDEI.PLEGDED
Retrocopy EEHSAVVPDEITPLEGDED

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	0.02 RPM	954.68 RPM
bodymap2_adrenal	0.33 RPM	827.93 RPM
bodymap2_brain	0.12 RPM	1363.37 RPM
bodymap2_breast	0.10 RPM	831.55 RPM
bodymap2_colon	0.19 RPM	2204.15 RPM
bodymap2_heart	0.83 RPM	593.10 RPM
bodymap2_kidney	0.31 RPM	911.35 RPM
bodymap2_liver	0.02 RPM	294.49 RPM
bodymap2_lung	0.11 RPM	1498.12 RPM
bodymap2_lymph_node	0.88 RPM	1394.39 RPM
bodymap2_ovary	0.67 RPM	2074.32 RPM
bodymap2_prostate	0.62 RPM	1329.78 RPM
bodymap2_skeletal_muscle	0.18 RPM	1193.65 RPM
bodymap2_testis	0.23 RPM	1191.52 RPM
bodymap2_thyroid	0.02 RPM	2048.01 RPM
bodymap2_white_blood_cells	0.37 RPM	545.45 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2912 was not detected

EST

No EST(s) were mapped for retro_hsap_2912 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_139741	751 libraries	834 libraries	242 libraries	1 library	1 library

The graphical summary, for retro_hsap_2912 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_2912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2912 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1968
Pongo abelii	retro_pabe_2425
Macaca mulatta	retro_mmul_1869

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 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,
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,
Rattus norvegicus	ENSRNOG00000019834	6 retrocopies	retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tursiops truncatus	ENSTTRG00000006924	1 retrocopy	retro_ttru_292,