RetrogeneDB ID: retro_ptro_2003

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:90151506..90153673(+)
• 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_2003
ATGCCTGAGGAAGTGCACCATGGAGAGGAGGAGGTGGAGACTTTTGCCTTTCAGGCAGAAATTGCCCAACTCATATCCCT
CATCATCAATACCTTCTATTCCAACAAGGAGATTTTCCTTCAGGAGTTGATCTCTAATGCTTCTGATGCCTTTGACAAGA
TTCGCTATGAGAGCCTGACAGACCCTTTGAAGTTGGACAGTGGTAATGAGCTGAAAATTGACATCATCCCCAACCCTCAG
GAACGTACTCTGGCTTTGGTAGACACAGGCATTGGCATGACCAAAGCTGATCTCATAAATAATTTGAGAATCATTGCCAA
GTCTGGTACTAAAGCATGCATGGAGGCTCTTCAGGCTGGTGCAGACATCTCCATGATTGGGCAGTTTGGTGTTGGCTTTT
TTCTGCCTACCTGGTGGCAGAGAAAGTGGTTGTGATCACAAAGCACAACGATGATGAACAGTATGCTTGGGAGTCTTCTG
CTGGAGGTTCCTTCACTGTGCATGGTGACCATGGTGAGCCCATTGGCAGGGGTACCAAAGTGATCCTCCATCTTAAAGAA
GATCAGACAGAGTACTTAGAAGAGAGGCAGGTCAAAGAAGTAGTGAAGAAGCATTCTCAGTTCATAGGCTATCCCATCAC
CCTTTATTTGGAGAAGAAACAAGAGAAGGAAATTAGTGATGATGAGGCAGAGGAAGAGAAAGGTGAGAAAGAAGAGGAAG
ATAAAGATGACGAAGAAAAGCCCAAGATCGAAGATGTGGGTTCAGATGAGGAGGATGACAGCAGTAAGGATAAGAAGAAG
AAAACTAAGAAGATCAAAGAGAAATACATTGACTAGGAAGAACTAAACAAGACCAAGCCTATTTGGACCAGAAACCATGA
TGACATCACCCAAGAGGAGTATGGAGAATTCTATAAGAGCCTCACCAGTGACTGGGAAGACCACTTGGCACTCAAGCACT
TTTCTGTAGAAGGTCAGTTGGAATTCAGGGCATTGCTATTCAGTCCTCGTCGGGCTCCCTTTGACCTTTTTGAGAACAAG
AAGGAAAAGAACAACATCAAACTGTATGTCCGCCATGTGTTCATCATGGACAGCTGTGATGAGTTGATACCAGAGTATCT
CAATTTTATCCATGGTGTGGTTGACTGAGGATCCGCCCCTGAACATCTCCCGAGAAATGCTCCAGCAGAGAAAATCTTGA
AAGTCATTCGCAAAAACATTGTTAAGAAGTGCCTTGAGCTCTTCTCTGAGCTGGCAGAAGATAAGGAGATTATAAGAAAT
TCTATGAGGCATTTTCTAAAAATCTCAAGCTTGGAATCCACAAAGACTCCACTAACCGCCGCCGCCTGTCTGAGCTGCTG
CGCTATCACACCTCCCAGTCTGGAGATGAGAGGACATCTCTGTCAGAGTATGTTTCTCACATGAAGGAGACACAGAAGTC
CACCTATTACATCACTGGTGAGAGCAAAGAGCAGGTGGCCAACTCTGCTTTTGTGGAGCGAGTGCGGAAACGGGGCTTCG
AGGTAGTATATATGACTGAGCCCATTGACGGGTACTGTGTGCAGCAGCTCAAGGAGTTTGATGGGAAAAGCCTGGTCTCA
GTTACCAAGGAGGGTCTGGAGCTGCCTGAGGATGAGGAGGAGAAGAAGAAGATGGAAGACAGCAAGGCAAAGTTTGAGAA
CCTCTGCAAGCTCATGAAAGAAATCTTAGATAAGAAGGTCGAGAAGGTGACAATCTCCAATAGACTTGTGTCTTCACCCT
GCTGCATTGTGACCAGCACCTACGGCTGGACAGCCAATATGGAGTGGATCATGAAAGCCCAGGCACTTTGGGACAACTCC
ACCATGGGCTATATGATGGCCAAAAAGCACCTGGAGATCAACCCCGACCACCCCATCGTGGAGACGCTGCGGCAGAAGGC
TGAGGCCGACAAGAATGATAAGGCAGTTAAGGACCTGGTGGTGCTGCTGTTTGAAACCGCCCTGCTATCTTTGGGCTTTT
CCCTTGAGGATCCCCAGACACACTCCAACCACATCTACCACATGATCAAGCTAGGTCTAGGTATTGATGAAGATGAAGTG
GCAGCAGAGGAACCCAATGATGCAGTTCCTGATGCGATCCCCCCTCTTGAGGGTGATGAGGATGCGTCTCGCATGGAAGA
AGTCGAA

Alignment

ORF - retro_ptro_2003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKE
          MPEEVHHGEEEVETFAFQAEIAQL.SLIINTFYSNKEIFL.ELISNASDA.DKIRYESLTDP.KLDSG.E
Retrocopy MPEEVHHGEEEVETFAFQAEIAQLISLIINTFYSNKEIFLQELISNASDAFDKIRYESLTDPLKLDSGNE

Parental  LKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFY-SAYLV
          LKIDIIPNPQERTL.LVDTGIGMTKADLINNL..IAKSGTKA.MEALQAGADISMIGQFGVGF..SAYLV
Retrocopy LKIDIIPNPQERTLALVDTGIGMTKADLINNLRIIAKSGTKACMEALQAGADISMIGQFGVGFF<SAYLV

Parental  AEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFI
          AEKVVVITKHNDDEQYAWESSAGGSFTV..DHGEPIGRGTKVILHLKEDQTEYLEER.VKEVVKKHSQFI
Retrocopy AEKVVVITKHNDDEQYAWESSAGGSFTVHGDHGEPIGRGTKVILHLKEDQTEYLEERQVKEVVKKHSQFI

Parental  GYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQ
          GYPITLYLEK..EKEISDDE.................KPKIEDVGSDEEDDS.KDKKKKTKKIKEKYID.
Retrocopy GYPITLYLEKKQEKEISDDEXXXXXXXXXXXXXXXXXKPKIEDVGSDEEDDSSKDKKKKTKKIKEKYID*

Parental  EELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKK
          EELNKTKPIWTRN.DDITQEEYGEFYKSLT.DWEDHLA.KHFSVEGQLEFRALLF.PRRAPFDLFENKK.
Retrocopy EELNKTKPIWTRNHDDITQEEYGEFYKSLTSDWEDHLALKHFSVEGQLEFRALLFSPRRAPFDLFENKKE

Parental  KNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSEL
          KNNIKLYVR.VFIMDSCDELIPEYLNFI.GVVD....P....R......KILKVIRKNIVKKCLELFSEL
Retrocopy KNNIKLYVRHVFIMDSCDELIPEYLNFIHGVVD*GSAPEHLPRN-APAEKILKVIRKNIVKKCLELFSEL

Parental  AEDKE-NYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITG
          AEDKE..YKKFYEAFSKNLKLGIH.DSTNRRRLSELLRYHTSQSGDE.TSLSEYVS.MKETQKS.YYITG
Retrocopy AEDKE<DYKKFYEAFSKNLKLGIHKDSTNRRRLSELLRYHTSQSGDERTSLSEYVSHMKETQKSTYYITG

Parental  ESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKA
          ESKEQVANSAFVERVRKRGFEVVYMTEPID.YCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKME.SKA
Retrocopy ESKEQVANSAFVERVRKRGFEVVYMTEPIDGYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEDSKA

Parental  KFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEI
          KFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANME.IMKAQAL.DNSTMGYMMAKKHLEI
Retrocopy KFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMEWIMKAQALWDNSTMGYMMAKKHLEI

Parental  NPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAE
          NPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLS.GFSLEDPQTHSN.IY.MIKLGLGIDEDEVAAE
Retrocopy NPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSLGFSLEDPQTHSNHIYHMIKLGLGIDEDEVAAE

Parental  EPSAAVPDEIPPLEGDEDASRMEEVD
          EP..AVPD.IPPLEGDEDASRMEEV.
Retrocopy EPNDAVPDAIPPLEGDEDASRMEEVE

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	1.25 RPM	760.70 RPM
SRP007412_cerebellum	1.51 RPM	860.72 RPM
SRP007412_heart	1.22 RPM	769.78 RPM
SRP007412_kidney	0.78 RPM	589.46 RPM
SRP007412_liver	1.80 RPM	666.44 RPM
SRP007412_testis	0.63 RPM	413.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2003 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2003 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2958

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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,