RetrogeneDB ID: retro_ptro_1850

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:188147024..188148196(+)
• 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_1850
AGAAGAGCTCTTTTTGTTTCAAGATGTGCTCCTTTTGACCTATTTGAAAACAGAAAGAAAAAGAACAACATTCAGTTGTA
TGTACGCAGAGTTTTCATCATGGGTAACTGTGAGGAGCTAATCCCTGAATACCTGAACTTCATTAGAGGGGTGATGGACT
CAGAGGATCTCCCTCTAAATATTTTTTCTGAGATGTTGCAACAAAGCAAAATTTTGAAAGTTATTAGGAAGAATTTGGTC
AAAACATACTTAGAACTCTTTGCTGAACTGGCAGAGGATAAAAAGAACTACAAAAAGTTCTACAAGAAGTTATCTAAAAA
CATAAATCTTTGAATATATAGACTCTCAAAATCAGAAGAAGCTTTCAGAGCTGTTGAAATAGTGCACATCTGCCTCTGGT
GATGAGATGGTTTATCTCATTGTGTTTTCCAGAATGAAGGCAAACCAGAAACATATCTACTACATTACAGGTGAGACCAA
GGACCAAGTAGCTAACTCAGCCTTTGTGGAATGTCTTCAGAAGCGTGGCTTAGAAGTGATCTACATGATCGAGTTGATTG
ATAAGTACTGTGTCCAGCAGCTGAAGGAATTTGAGAGTAAGACTGTAGTGTCAGTTGCCAAAGAGGGTTTGGAACTTCCA
GAAGATGAAGAAGAAAACAAGAAACAGGAAGAGAAAAAAACAAAGTTTGAGAACCTCTGCAAAATCATGAAAGACATGTT
GGAGAAAAAAGTCAAAAAGGTGGTTGTGTCAAACTGGTGACATCCCCATGCTGTATTGTCACAAGCACATATGGCTGGAC
AGCAAACGTGGAAAGAATCATGAAAGCTCAAGCCCTGTGAGACAACTCAACAATGGGCTACATGGCAGCAAAGAAACACC
TGGAGATAAACCCTGACCATTCATGATTGAAACCTTAAGGCAAAAGGCAGAGGCTGATAAGAACAACAAGTCAGTGAAGG
ATCTGGTCATCTTGCTTTACTAAACTGCACTCCCATCTCCTGGCTTCAGTATGGAAGACCCTCAGAGACATACTAACAAG
ATCTATAGGATGATCAAACTTGGTCTGGGTATTGATGAATATGATCCTACTGCTAATGGTATCAATGCCGCTATAACTAA
AGAAATGCCGCCCCTCAGAGGAGGTGATGACACATCACGCATGGAAGAAGTA

Alignment

ORF - retro_ptro_1850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.84 %
• Parental protein coverage: 54.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSK
          R..LF..R.APFDLFEN.KKKNNI.LYVRRVFIM..C.ELIPEYLNFIRGV.DSEDLPLNI..EMLQQSK
Retrocopy RRALFVSRCAPFDLFENRKKKNNIQLYVRRVFIMGNCEELIPEYLNFIRGVMDSEDLPLNIFSEMLQQSK

Parental  ILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTN-RR-RLSELLRYHTSQSGDEMT
          ILKVIRKN.VK..LELF.ELAEDK.NYKKFY...SKN..L.I...S...RR..LSELL...TS.SGDEM.
Retrocopy ILKVIRKNLVKTYLELFAELAEDKKNYKKFYKKLSKNINL*IYRLSKS<RR<KLSELLK*CTSASGDEMV

Parental  SLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVT
          .L....SRMK..QK.IYYITGE.K.QVANSAFVE...KRG.EV.YM.E.ID.YCVQQLKEF..K..VSV.
Retrocopy YLIVF-SRMKANQKHIYYITGETKDQVANSAFVECLQKRGLEVIYMIELIDKYCVQQLKEFESKTVVSVA

Parental  KEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISN-RLVSSPCCIVTSTYGWTANMERIM
          KEGLEL................FENLCK.MK..L.KKV.KV..SN....S..C.IVTSTYGWTAN.ERIM
Retrocopy KEGLELXXXXXXXXXXXXXXXXFENLCKIMKDMLEKKVKKVVVSN<LVTSPCC-IVTSTYGWTANVERIM

Parental  KAQALRDNSTMGYMMAKKHLEINPDHP-IVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQT
          KAQAL.DNSTMGYM.AKKHLEINPDH....ETLRQKAEADKN.K.VKDLV.LL..TAL.S.GFS.EDPQ.
Retrocopy KAQAL*DNSTMGYMAAKKHLEINPDHS<MIETLRQKAEADKNNKSVKDLVILLY*TALPSPGFSMEDPQR

Parental  HSNRIYRMIKLGLGIDEDEVAAEEPSAAVPDEIPPLEGDEDASRMEEV
          H.N.IYRMIKLGLGIDE....A....AA...E.PPL.G..D.SRMEEV
Retrocopy HTNKIYRMIKLGLGIDEYDPTANGINAAITKEMPPLRGGDDTSRMEEV

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	0.05 RPM	760.70 RPM
SRP007412_cerebellum	0.04 RPM	860.72 RPM
SRP007412_heart	0.00 RPM	769.78 RPM
SRP007412_kidney	0.03 RPM	589.46 RPM
SRP007412_liver	0.03 RPM	666.44 RPM
SRP007412_testis	0.11 RPM	413.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1850 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1850 has 0 orthologous retrocopies within eutheria group .

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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,