RetrogeneDB ID: retro_ptro_207

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:136849421..136850739(+)
• 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_207
TACATCGATCAAGAAAAACTCAACAAAACAAAGCCCATCTGGACCAGAAATCCTGATGATATTACTAATGAGGAGTAAGA
ATTCTACAAGAGCTTGACCAATGACTGGGAAGATCATTGGCAGTGAAGCATTTTTCAGTTGAAGGACACTTGGAATTCAG
AGCCCTTCTATTTGTCCCACAACATGCTCCTTTTGACTTGTTTGGAAAGAGAGAGAAAAAGAACATCAAATTGTATGTAC
ACAGAGTTTCCATCATGGCTAACTGTGAGGAGCTAATCCCTGCGTATCTGAACGTCATTGGAAAGGTGGTGGACTCAGAG
GATCTCCGTCTAAATGTTTCCCATGAGATGTTGTGACAAAGCAAAATTTTGGAAGTTATCAGGAAGAATTTGGTCAAAAA
ATGCTTAGAACTCTTTACCAAACTGGCAGAAGATAAAGAGAACTACAAGAAATTCTATGAGCAGTTCTCTAAAAGCGTAA
AGCTTGAAATATACGAAGACTCTCAACATTGGAAGAAGTTTTCAGAGCTGTTAAGATACTACACATCTGCTTCTGGTGAT
GAGATGGTTTCTCTCAAGGACTACTGCACCAGAATGAAGGAAAACTAGAAACATATCTATTACATCACAGGTGAGACCAA
GAACCAGGTAGCTAAATTTGTGGAATGTCTTCGGAAACATGGCTTAGAAGTGATCTATATGATCAAGCCAATTGATGAGT
ACTGTGTCCAACACTGAAGGAATTTGAGGGGAAGACTTTAGTGTCAGTCACCAAAGAGGGCTTGGAACTTCCAGAGGATG
AAGAAGAAAAAAAGAAACAGGAAGAGAAAAAAACAAAGTTTGAGAACATCTGCAAAATCATGAAAGACATATTGGAGAAA
AAAGTTGAAAAGGTGGTTGTGTCAAACTGATTGGTGAAGTCTCCATGCTATATTGTCACGAGCATATATGGCTGGACAGC
AAACATGGAAAGAATCATGAAAACTCAAGCCCTAAGAGACAACTCAACAATGGGTTACATGGCAGCAAAGAAACACCTGG
AGATAAACCCTGACCATTCCATTATTGAGACCTTAAGGCAAAAGGCAGAGGCAGATAAGTACAAGTCTGTGCAGGATCTG
GTCATCTTGCTTTACAAAACTGCTCTTTTGTCTTCCGGCTTTGGTCTGGAAGATCCCCAGACACATGCTAACAGGATCTA
CAGGATGATCAAACTTGGTGTGGGTATTGATGAAAATGACCCTACTGCTGATGATACTGCTGAAGAAATGTCACCCCTTG
AAGGGGACAATGACACATCATGCATGGAAGAAACAGAC

Alignment

ORF - retro_ptro_207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.37 %
• Parental protein coverage: 61.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDH-LAVKHFSVEGQLEFRALLFVPRRAPFDLF
          YIDQE.LNKTKPIWTRNPDDITNEE..EFYKSLTNDWEDH.LAVKHFSVEG.LEFRALLFVP..APFDLF
Retrocopy YIDQEKLNKTKPIWTRNPDDITNEE*-EFYKSLTNDWEDH<LAVKHFSVEGHLEFRALLFVPQHAPFDLF

Parental  ENRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLE
          ..R.KKN.IKLYV.RV.IM.NCEELIP.YLN.I..VVDSEDL.LN.S.EML.QSKIL.VIRKNLVKKCLE
Retrocopy GKREKKN-IKLYVHRVSIMANCEELIPAYLNVIGKVVDSEDLRLNVSHEML*QSKILEVIRKNLVKKCLE

Parental  LFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIY
          LFT.LAEDKENYKKFYEQFSK..KL.I.EDSQ..KK.SELLRYYTSASGDEMVSLKDYCTRMKEN.KHIY
Retrocopy LFTKLAEDKENYKKFYEQFSKSVKLEIYEDSQHWKKFSELLRYYTSASGDEMVSLKDYCTRMKEN*KHIY

Parental  YITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQ-LKEFEGKTLVSVTKEGLELPEDEEEKKKQ
          YITGETK.QVA...FVE.LRKHGLEVIYMI.PIDEYCVQ..LKEFEGKTLVSVTKEGLELPED.......
Retrocopy YITGETKNQVAK--FVECLRKHGLEVIYMIKPIDEYCVQH<LKEFEGKTLVSVTKEGLELPEDXXXXXXX

Parental  EEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAK
          ......FEN.CKIMKDILEKKVEKVVVSN.LV.SPC.IVTS.YGWTANMERIMK.QALRDNSTMGYMAAK
Retrocopy XXXXXXFENICKIMKDILEKKVEKVVVSN*LVKSPCYIVTSIYGWTANMERIMKTQALRDNSTMGYMAAK

Parental  KHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGIDED
          KHLEINPDHSIIETLRQKAEADK..KSV.DLVILLY.TALLSSGF.LEDPQTHANRIYRMIKLG.GIDE.
Retrocopy KHLEINPDHSIIETLRQKAEADKY-KSVQDLVILLYKTALLSSGFGLEDPQTHANRIYRMIKLGVGIDEN

Parental  DPTADDTSAAVTEEMPPLEGDDDTSRMEEVD
          DPTADDT.....EEM.PLEGD.DTS.MEE.D
Retrocopy DPTADDTA----EEMSPLEGDNDTSCMEETD

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	0.21 RPM	1070.46 RPM
SRP007412_cerebellum	0.14 RPM	836.99 RPM
SRP007412_heart	0.12 RPM	692.34 RPM
SRP007412_kidney	0.13 RPM	1038.98 RPM
SRP007412_liver	0.00 RPM	494.25 RPM
SRP007412_testis	0.63 RPM	2686.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_207 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_207 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_237
Pongo abelii	retro_pabe_415

---

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,