RetrogeneDB ID: retro_ptro_880

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:97084711..97086679(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AB1
• Ensembl ID: ENSPTRG00000018217
• Aliases: None
• Description: heat shock protein 90kDa alpha (cytosolic), class B member 1 [Source:HGNC Symbol;Acc:5258]

Sequence

>retro_ptro_880
ATGTCTGAGGAAGTACACCATGGAGAGGAGGAGGTGGAGACTTTTGCCTTTCAGACAGAAATTGCCCAACTCAGGTCTCT
TATTATCAATATTTTCTATTCCAACAAGCAGATTTTTCCTTCAAGTGTTGATTTCTAATGCTTCTGATGCCTTGGACAAG
ATTCTCTATGAGAGACTGGCAGACACTTACAAGTTGGACAGTAGTAAAGAGCTGAAAATTGACATCATGCCCAACCCTCA
GGAATACACCCTGACTTTGGTGGACACAGGCATTTGCATGACAAAGTTGATTTCATAAATAATTCGGGAACCATTGCCAA
GTCTGAGACTAAAGGATTTATGGAGGCTCTTCAGGCTGGTGCAGACATCTCCATGATTGTCAATTTGGTGTTGGCTTTCA
TTCTGCCTATCTGGTGGCAGAGAAAGTGGTTGTGATCACAAAGCACAATGATGATGAACAGTGAGCCTGGGAGTTTTCTG
GTGGGGGTTCCTTCACTGTATGTGCTGACCACGGCAGAGGTACCAAAATGATCCTCCACCTTAAAGAAAACCAGACAGAG
TACTTAGAAGAGAGATGGGTCAAAGACGCAGTGAAAAAGCACTCACAGTTCATAGGCTAACCCATCACCCTCTATCTGAG
GAAGGAAAGAGAGAAGGAAATCAGTGATGATGAGGCAGAGGAAGAGAAAGGCAAGAAATAATAGGAAGATAAATATAATG
AGGAAAAACCCAAGATTGAAAATGTGGGTTCAAATGAGGAGGATGGAAGTGGTAAGGATAAGAAAAAGAAAACCGAGAAG
ATCAAAGAGAAATACATTAATCAGGAAGAACTAAACAAGATCAAGACTATTTGGACAAGAAACCATGATTACATCACCCA
GGAGTATGGAGAATTCTGTAACAGCCACACTAATGCCTGGGAAGACCACTTGGCAGTCAAGCACTTCTCTATAGAAGGTC
AGTTGGAATTCAGGGCGTTGTTGTTCATCCCTTATCGGGCTCCTTTTGACCTCTTTGAGAACAATAAGAATAAAGACACC
ATCAAACTCTACGTCCTTCATGTGTTCATCGTGCACAGCTGTGATGAGTTGATACCAGAGGATCTCAACTTTATCTGTGG
TATGGTTGACTCTGAGGATCTACCCCTGAACATTTGAGAAATGCTCCAGGAGAGCAAAATCTTGAAAGTAGTTCACAGAA
ACATTGTTAACTGGTGCCTTGAGCTCTTCTCTAAGTTGGCAGAAGACAAAGAGAGTTACAAGAAATTCTATGAGGCATTC
TCTAAAAATCTAATGTTTGGAATCCCCGAGGACTCCCCTAACTGGCGACACCTGTCTGAGCTGCTGCACTTTCACAGCTC
CCAGTCTGGAGATGGGATGACATCTCTGTTAGAATATGTCTCTTGCATGAAGGAGACACGGAAATCCACCTACTACATCA
CTGGTGAGAGCAACGAACAGGTGGCCAGCTCTGCTTTCGTGGAGTGAGTGCGGAAGCAGGCCTTTGAGGTAGTGCATATG
ACCAACCCCACTGATGAGTACTGCATGCAGCAGCTCAAGGAGTTTGATGGGAAGTGCCTCGTCTCAGTTACCAAGGAGGG
TCTGGAGCTACCAGAGGGTGAGGAGGAGAAGAAGAAAATGGAAGAGTGCAAGGTGAAGCTTGAGAACCTCGGCAAGTCCA
TGAAAATAATCTTGGATAAGAAGGCTGAGAAGGTGACAGCCTCCAATAGACTTGAATCTTCACCGGCTGCATTTTGACAA
CCATCTATGGCTTGACAGCCATTATGGAGCAGATTGTGAAAGCCCAGGCACTTTGGGACAACTCTATGATGGGTTACGTG
ATGGCCAAAGAGAACCTGGAGATCAACATGACTACACTATTGTGGAGACGCTGTGGCAGAAGGCTGAGGCGGACAAGAAC
GACAAGGCTGTCAAGGACCGGGTGGTGCTGCTGTTGAAAACCAAGCTG

Alignment

ORF - retro_ptro_880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.04 %
• Parental protein coverage: 91.57 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIF-LRELISNASDALDKIRYESLTDPSKLDSGK
          M.EEVHHGEEEVETFAFQ.EIAQL.SLIIN.FYSNK.IF.L..LISNASDALDKI.YE.L.D..KLDS.K
Retrocopy MSEEVHHGEEEVETFAFQTEIAQLRSLIINIFYSNKQIF>LQVLISNASDALDKILYERLADTYKLDSSK

Parental  ELKIDIIPNPQERTLTLVDTGIGMTK-ADLINNLGTIAKSGTKAFMEALQAGADISMIG-QFGVGFYSAY
          ELKIDI.PNPQE.TLTLVDTGI.MTK..D.INN.GTIAKS.TK.FMEALQAGADISMI..QFGVGF.SAY
Retrocopy ELKIDIMPNPQEYTLTLVDTGICMTK<VDFINNSGTIAKSETKGFMEALQAGADISMIV<QFGVGFHSAY

Parental  LVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQ
          LVAEKVVVITKHNDDEQ.AWE.S.GGSFTV.ADH....GRGTK.ILHLKE.QTEYLEER.VK..VKKHSQ
Retrocopy LVAEKVVVITKHNDDEQ*AWEFSGGGSFTVCADH----GRGTKMILHLKENQTEYLEERWVKDAVKKHSQ

Parental  FIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYI
          FIG.PITLYL.KEREKEISDDEAEEEKG.K..EDK..EEKPKIE.VGS.EED.SGKDKKKKT.KIKEKYI
Retrocopy FIG*PITLYLRKEREKEISDDEAEEEKGKK**EDKYNEEKPKIENVGSNEEDGSGKDKKKKTEKIKEKYI

Parental  DQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENK
          .QEELNK.K.IWTRN.D.ITQE.YGEF..S.TN.WEDHLAVKHFS.EGQLEFRALLFIP.RAPFDLFEN.
Retrocopy NQEELNKIKTIWTRNHDYITQE-YGEFCNSHTNAWEDHLAVKHFSIEGQLEFRALLFIPYRAPFDLFENN

Parental  KKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFS
          K.K..IKLYV..VFI..SCDELIPE.LNFI.G.VDSEDLPLNI..EMLQ.SKILKV...NIV..CLELFS
Retrocopy KNKDTIKLYVLHVFIVHSCDELIPEDLNFICGMVDSEDLPLNI*-EMLQESKILKVVHRNIVNWCLELFS

Parental  ELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYIT
          .LAEDKE.YKKFYEAFSKNL..GI.EDS.N.R.LSELL..H.SQSGD.MTSL.EYVS.MKET.KS.YYIT
Retrocopy KLAEDKESYKKFYEAFSKNLMFGIPEDSPNWRHLSELLHFHSSQSGDGMTSLLEYVSCMKETRKSTYYIT

Parental  GESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESK
          GES.EQVA.SAFVE.VRK..FEVV.MT.P.DEYC.QQLKEFDGK.LVSVTKEGLELPE.EEEKKKMEE.K
Retrocopy GESNEQVASSAFVE*VRKQAFEVVHMTNPTDEYCMQQLKEFDGKCLVSVTKEGLELPEGEEEKKKMEECK

Parental  AKFENLCKLMKEILDKKVEKVTISNRLVSSPC-CIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHL
          .K.ENL.K.MK.ILDKK.EKVT.SNRL.SSP..CI.T..YG.TA.ME.I.KAQAL.DNS.MGY.MAK..L
Retrocopy VKLENLGKSMKIILDKKAEKVTASNRLESSPA<CILTTIYGLTAIMEQIVKAQALWDNSMMGYVMAKENL

Parental  EIN-PDHPIVETLRQKAEADKNDKAVKDLVVLLFETAL
          EIN..D..IVETL.QKAEADKNDKAVKD.VVLL..T.L
Retrocopy EIN<HDYTIVETLWQKAEADKNDKAVKDRVVLLLKTKL

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_prefrontal_cortex	0.00 RPM	760.70 RPM
SRP007412_cerebellum	0.00 RPM	860.72 RPM
SRP007412_heart	0.00 RPM	769.78 RPM
SRP007412_kidney	0.00 RPM	589.46 RPM
SRP007412_liver	0.00 RPM	666.44 RPM
SRP007412_testis	0.00 RPM	413.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_880 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_880 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_880 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1011
Macaca mulatta	retro_mmul_1319

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Otolemur garnettii	ENSOGAG00000011961	1 retrocopy	retro_ogar_2574,
Pongo abelii	ENSPPYG00000016655	2 retrocopies	retro_pabe_2425, retro_pabe_415,
Pan troglodytes	ENSPTRG00000005372	1 retrocopy	retro_ptro_170,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Pan troglodytes	ENSPTRG00000018217	4 retrocopies	retro_ptro_1850, retro_ptro_1968, retro_ptro_2003, retro_ptro_880 ,
Tupaia belangeri	ENSTBEG00000014873	1 retrocopy	retro_tbel_1428,