RetrogeneDB ID: retro_ptro_1968

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:13107651..13109044(+)
• 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_1968
GTGGGTTCAGATGAGGAGGATGACAGTGGTAAGGATAAGAAGAAGAAAACTAAGAAGATCAAAGAGAAATACATTGATCA
GGAAGAACTAAACAAGACCAAGCCTATTTGGACCAGAAACACTGAAGACATCACCCAAGAGGAGTATGGAGAATTCTGTA
AGAGCCTCACCAATGACTGGAAAGACCACTTGGCAGTCAGGTACTTTTCTGTAGAAGGTCAGTTGGAATTCAGGGCATTG
CTATTCATACCTCCTTAGGCTCCCTTTCATCTTTTTGAGAACAAGAAGAAAAAGAACAACATCAAACTCTATGTCCATCG
TGTGTTCATCAGGGACAGCTGTGATGAGTTGATACCAGAGTGTCTCAACTTTATCTGTGGTGTGGTTGACTCTGAGGATT
TCCCCTGAACATCTCCTGAGAAATGCTCCAGCAGAGCAAAATCTTGAAAGTCATTCACAGAAACATTGTTAAGAAGTGCC
TTGAGCTCTTCACTGAGCTGCTGGAAGACAAGGAGAATTACATGAAATTCTATGAGGCATTCTCTAAAAATCTCAAGCTT
GGAATCCACAAGGACTCCACTAACTGATGCCACCCATCTGAGCTGCTGTGTTATCACACCTCCCAGTCTGGAGATGAGAT
GATATCTTTGTTAGAGTATGTTTCTCACATGAAGGAGATACAGAAGTCCATCTATTACATCACTGGTGAGAGCAAAGAGC
AGGTTGCCAACTCAGCTTTTGTGGAGCAAGTATGGAAGCGGGGCTTCAGGGTGGTATATATGATCGAGCCCATTGATGGC
TACGTGTGCAGCAACTCAAGGAGTTTGATGGGAAGAGCCTGGTCTCAGTTACCAAGGAGGGCCTGGAGCTACCTGAGGAT
GGGGAGGAGAAGAAGAGAATGGAAGAGAGGAAGGCAAAGTTTGAGAACCTCTGCAAGTTCATGAAAGAAACCTTAGATAA
GAAGGTTGAGATGGTGACAGTCTCCAACAGGCTTGTGTCTTCATCCTGCTGCATTGTGACCAGCACCTACAGCTAGACAG
CCAATATGGAGCAGATCATGAAAGCCCAGGCACTTCGGGTCAACTCCACTGTGGGCTATATGATGGCCAAAAAGCACCTG
GAGATCAACCCCAACCACCCCATTGTGGAGACACTGCAGCAGAAGGCTGAGGCACACAAGAATGACAAGGCAGTCAAGGA
CCTGGTGGTGCTGCCGTTAGAAACTGCCTTGCTGTCTTCTGGCTTTTCCCTTGAGGATCCCCAGACCCATTCCAACCACA
ACTACTGCATGATCAACCTAGGTCTAGGTATCGATGAAGATTAAGTGACAGCAGAGGAACACAGTGCTGTGGTTCCTGAT
GAGATCACCCCTCTTGAGGGTGACGAGGATGCG

Alignment

ORF - retro_ptro_1968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.08 %
• Parental protein coverage: 64.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFS
          VGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRN..DITQEEYGEF.KSLTNDW.DHLAV..FS
Retrocopy VGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNTEDITQEEYGEFCKSLTNDWKDHLAVRYFS

Parental  VEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLP-LNIS
          VEGQLEFRALLFIP..APF.LFENKKKKNNIKLYV.RVFI.DSCDELIPE.LNFI.GVVDSED.P.LNIS
Retrocopy VEGQLEFRALLFIPP*APFHLFENKKKKNNIKLYVHRVFIRDSCDELIPECLNFICGVVDSEDFP<LNIS

Parental  REMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQ
          .EMLQQSKILKVI..NIVKKCLELF.EL.EDKENY.KFYEAFSKNLKLGIH.DSTN....SELL.YHTSQ
Retrocopy *EMLQQSKILKVIHRNIVKKCLELFTELLEDKENYMKFYEAFSKNLKLGIHKDSTN*CHPSELLCYHTSQ

Parental  SGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYC-VQQLKEFDG
          SGDEM.SL.EYVS.MKE.QKSIYYITGESKEQVANSAFVE.V.KRGF.VVYM.EPID.Y..VQQLKEFDG
Retrocopy SGDEMISLLEYVSHMKEIQKSIYYITGESKEQVANSAFVEQVWKRGFRVVYMIEPIDGYV<VQQLKEFDG

Parental  KSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTA
          KSLVSVTKEGLELPED.EEKK.MEE.KAKFENLCK.MKE.LDKKVE.VT.SNRLVSS.CCIVTSTY..TA
Retrocopy KSLVSVTKEGLELPEDGEEKKRMEERKAKFENLCKFMKETLDKKVEMVTVSNRLVSSSCCIVTSTYS*TA

Parental  NMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSL
          NME.IMKAQALR.NST.GYMMAKKHLEINP.HPIVETL.QKAEA.KNDKAVKDLVVL..ETALLSSGFSL
Retrocopy NMEQIMKAQALRVNSTVGYMMAKKHLEINPNHPIVETLQQKAEAHKNDKAVKDLVVLPLETALLSSGFSL

Parental  EDPQTHSNRIYRMIKLGLGIDEDEVAAEEPSAAVPDEIPPLEGDEDA
          EDPQTHSN..Y.MI.LGLGIDED.V.AEE.SA.VPDEI.PLEGDEDA
Retrocopy EDPQTHSNHNYCMINLGLGIDED*VTAEEHSAVVPDEITPLEGDEDA

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	0.04 RPM	760.70 RPM
SRP007412_cerebellum	0.11 RPM	860.72 RPM
SRP007412_heart	0.23 RPM	769.78 RPM
SRP007412_kidney	0.05 RPM	589.46 RPM
SRP007412_liver	0.07 RPM	666.44 RPM
SRP007412_testis	0.42 RPM	413.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1968 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1968 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2912
Pongo abelii	retro_pabe_2425
Macaca mulatta	retro_mmul_1869

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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,