RetrogeneDB ID: retro_ptro_596

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:27771104..27773302(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AA1
• Ensembl ID: ENSPTRG00000006736
• Aliases: None
• Description: Pan troglodytes heat shock protein 90kDa alpha (cytosolic), class A member 1 (HSP90AA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001098572]

Sequence

>retro_ptro_596
ATGCCTGAGGAAACCCAGACCCAAAACCAACTGATGGAGGAGGAGGAGGTTGAGACATTCGCCTTTCAGGCAGAAATTGC
CCAGTTGATGTCATTGATCATCAATACTTTCTACTCGAACAAAGAGATCTTTCTGAGAGAGCTCATTTCAAATTCATCAG
ATGCATTGGACAAAATCTGGTATGAAAGCTTGACAGATCCCAGTAAATTAGACTCTGGGAAAGAGCTGCATATTAACCTT
ATACCAAACAAACAAGATCGAACTCTCACTATTGTGGATACTGGAATTGGAATGACCAAGGCTGACTTGATCAATAACCT
TGGTACTATCGCCAAGTCTGGGACCAAAGCGTTCATGGAAGCTTTGCAGGCTGGTGCAGATATCTCTATGATTGGCCAGT
TCGGTGTTGGTTTTTATTCTGCTTATTTGGTTGCTGAGAAAGTAACTGTGATCACCAAATATAATGATGATGAGCAGTAC
ACCTGGGAGTCCTCAGCAGGGGGATCATTCACAGTGAGGACAGACACAGGTGAACGTATGGGTCGTGGAACAAAGGTTAT
CCTACACCTGAAAGAAGACCAAACTGAGTACTTGGAGGAATGAAGAATAAAGGAGATTGTGAAGAAACATTCTCAGCTTA
TTGGATATCCCATTACTCTTTTTGTGGAGAAGGAATGTGATAAAGAAGTCAGCGACGATGAGGCTGAAGAAAAGGAAGAC
AAAGAAGAAGAAAAAGAAAAAGAAGAGAAAGAGTCCAAAGACAAACCTGAAATTGAAGATGTTGGTTCTGATGAGGAAGA
AGAAGAAAAGAAGGATGGTGACAAGAAGAAGAAGAAGAAGATTAAGGAAAAGTACATCGATCAAGAAGAACTCAACAAAA
CAAAGCCCATCTGGACCAGAAATCCCGACGATATTACTAATGAGGAGTACGGAGAATTCTACAAGAACTTGACCAATGAC
TGAGAAGATCACTTGGCAGTGATGCATTTTTCAGTTGAAGGACAGTTGGAATTCAGAGCCCTTCTATTTGTCCCATGACG
TGCTCCTTTTGACCTGTTTGAAAACAGAAAGAAAAAGAACAACATCAAATTGTATGTATGCAGAGTTTTCATCATGGATA
ACTGTGAGGAGCTAATCCCTGAATATCTGAACTTCATTAGAGGGGTGGTAGACTTGGAGGATCTCCCTCTAAACATTTCC
CGTGAGATGTTGCAACAAAGTAAAATTTTGAAAGTTATCAGGAAAAATTTGGTCAAAAAATGCTTAGAACTCTTTACAGA
ACTGGCGGAAGATAAAGAGAACTGCAAGAAATTCTATGAGCAGTTCTCTAAAAACATAAATCTTGGAATACAAGAAGACT
CTCAAAATCGGAAGAAGCTTTCAGAGCTGTTAAGGTACTACACGTCTGCCTCTGGTGATGAGATGGTTTCTCTCAAGGAC
TACTGCACCAGAATGAAGGAAAAACAGAAACATATCTATTATATCACAGGTGAGACCAAGGACCAGGTAGCTAACTCAGC
CTTTGTGGAACGTCTTGGGAAACATGGCTTAGAAGTGATCTATATGTTTGAGCCCATTGATGAGTACTGTGTCCAACAGC
TGAAGGAATTTGAGGGGAAGACTTTAGTGTCAGTCACCAAAGAAGGCCTGGAACTTCCAGAGGATGAAGAAAAGAAAAAG
AAATAGGAAGAGAAAAAACAATGTTTGAGAACCTCTGCAAAATCATGAAAGACATATTGGAGAAAAAAGTTGAAAAGGTG
GTTGTGTCAAACCGATTGGTGACGTCTCCATGCTGTATTGTCACAAGCACATATGGCTGGACAGAAAACATGGAGAGAAT
CATGAAAGCTCAAGCCCTAAGAGACAACTCAACAATGGGTTATATGGCAGCCAAGAAACACCTGGAGATAAATCCTGATG
ATTCCATTATTGAGACCTTAAGGCAAAAGGCAGAGGCTGATAAGAATGACAAGTCTGTGAAGGATCTGGTCATCTTGCTT
TACGAAACTGCACTCCTGTCTTCTGGCTTCAGTCTGGAAGATCCCCAGACACATGCTAACAGGACCTACAGGATGATCAA
ACTTGGTCTGGGTATTGATGAAGATGATCCTACTGCTGATGATACCAGTGCTGCTGTAACTGAAGAAATGCCGCCCCTCG
AAGGAGATGACGACACATCACGCATGGAAGAAGTAGAC

Alignment

ORF - retro_ptro_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.01 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKL
          MPEETQTQ.Q.MEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKI.YESLTDPSKL
Retrocopy MPEETQTQNQLMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIWYESLTDPSKL

Parental  DSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYS
          DSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYS
Retrocopy DSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYS

Parental  AYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKH
          AYLVAEKVTVITK.NDDEQY.WESSAGGSFTVRTDTGE.MGRGTKVILHLKEDQTEYLEE.RIKEIVKKH
Retrocopy AYLVAEKVTVITKYNDDEQYTWESSAGGSFTVRTDTGERMGRGTKVILHLKEDQTEYLEE*RIKEIVKKH

Parental  SQFIGYPITLFVEKERDKEVSDDEAEEKEDKEEEKEKEEKESEDKPQIEDVGSDEEEEEKKDGDKKKKKK
          SQ.IGYPITLFVEKE.DKEVSDDEA................S.DKP.IEDVGSDE...............
Retrocopy SQLIGYPITLFVEKECDKEVSDDEAXXXXXXXXXXXXXXXXSKDKPEIEDVGSDEXXXXXXXXXXXXXXX

Parental  IKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPF
          ....YIDQEELNKTKPIWTRNPDDITNEEYGEFYK.LTND.EDHLAV.HFSVEGQLEFRALLFVP.RAPF
Retrocopy XXXXYIDQEELNKTKPIWTRNPDDITNEEYGEFYKNLTND*EDHLAVMHFSVEGQLEFRALLFVP*RAPF

Parental  DLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKK
          DLFENRKKKNNIKLYV.RVFIMDNCEELIPEYLNFIRGVVD.EDLPLNISREMLQQSKILKVIRKNLVKK
Retrocopy DLFENRKKKNNIKLYVCRVFIMDNCEELIPEYLNFIRGVVDLEDLPLNISREMLQQSKILKVIRKNLVKK

Parental  CLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQK
          CLELFTELAEDKEN.KKFYEQFSKNI.LGI.EDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKE.QK
Retrocopy CLELFTELAEDKENCKKFYEQFSKNINLGIQEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKEKQK

Parental  HIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEEKK
          HIYYITGETKDQVANSAFVERL.KHGLEVIYM.EPIDEYCVQQLKEFEGKTLVSVTKEGLELPED.....
Retrocopy HIYYITGETKDQVANSAFVERLGKHGLEVIYMFEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDXXXXX

Parental  KQEEKKTKFENLCKIMKDILEKKVE-KVVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYM
          .............K..K....KK...KVVVSNRLVTSPCCIVTSTYGWT.NMERIMKAQALRDNSTMGYM
Retrocopy XXXXXXXCLRTSAKS*KTYWRKKLK<KVVVSNRLVTSPCCIVTSTYGWTENMERIMKAQALRDNSTMGYM

Parental  AAKKHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGI
          AAKKHLEINPD.SIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANR.YRMIKLGLGI
Retrocopy AAKKHLEINPDDSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRTYRMIKLGLGI

Parental  DEDDPTADDTSAAVTEEMPPLEGDDDTSRMEEVD
          DEDDPTADDTSAAVTEEMPPLEGDDDTSRMEEVD
Retrocopy DEDDPTADDTSAAVTEEMPPLEGDDDTSRMEEVD

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	2.48 RPM	1070.46 RPM
SRP007412_cerebellum	6.92 RPM	836.99 RPM
SRP007412_heart	6.91 RPM	692.34 RPM
SRP007412_kidney	4.16 RPM	1038.98 RPM
SRP007412_liver	3.37 RPM	494.25 RPM
SRP007412_testis	18.65 RPM	2686.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_596 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_596 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_859

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
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,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,