RetrogeneDB ID: retro_ptro_170

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:92403865..92405211(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90B1
• Ensembl ID: ENSPTRG00000005372
• Aliases: HSP90B1, TRA1
• Description: Pan troglodytes heat shock protein 90kDa beta (Grp94), member 1 (HSP90B1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246487]

Sequence

>retro_ptro_170
GAAGATGAATACAAAGCTTTTTACAAATCATTTTCAAAGGAAAGTGATGACCCCATGGCTTATATTCACTTTACCACTGA
AGGGGAAGTTACCTTCAAATCAATTTTATTTGTACCCACATCTGATCCACGTGGTCTATTTGATGAATATGGATCTAAAA
AGAGTGATTACATTAAGCTCTATGTGCTCTGTGTATTCATCACAGACGAATTCCACGATAGGATGCCTAAGTACCTTAAT
TTTGTCAAGGGTGTGGTGGACTCAGATGATCTCCCCTTGAATGTTTCCCTTGAGACTCTTCAGCAACATAAACTGCTTAA
GGTGATTAGGAAGAAGCTTGTTTGTAAAACTCTGGACAAGATCAAGAAGATTGCTGGTGAGAAATACAATGATAATTTTT
GGAAAGAATTTGGTACCAACATCAAGCTTGGTGTGATTGAAGACCACTCCAATCAAACATGTCTTGCTAAACTTCTTATG
TTCCAGTCTTCTCACCATCCAACTGACATTACTACACTAGACCAGTATGTGGAAAGAATGAAGGGAAAACAAGACAAAAT
CTACTTCATGGCTGGGTCCAGCAGAAAAGAGGCTGAATCTCCTCCATTTGTTGAACGACTTCTGAAAAAGGGCTATGAAG
TTATTTACCTCACAGAACCTGTGGATGAACACTGCATTCAGGCCTTTCCCAAATTTGATGGGAAGAGGTTCCAGAATGTT
GTCAAGGAAGGAATGAAGTTTGATAAAAGTGAGAAAACTAAGGAGAGTCATGAAGCAGTTGAGAAAGAATTTGAGCCTCT
GCTCAATTGGATGAAAGATAAAGCCCTTAAGGACAAAATTGAGAAGGCTGTGGTGTCTCAGCACCTGACAGAATCTCTGT
GTGCTTTGGTGGCCAGCCAGTACGGACGGTCTGGCAACACGGAGAGAATCATGAAAGCACAAGCATACCAAACGAGCAAG
GACAGCTCTACAAATTACTATGCAAGTCAGAAGAAAACATTTGAAATTAATCCCAGACACCCACTGATCAGAGACATGCT
TTGATGAATTAAGGAAGGTGAAGATGATAAAATAGTTTTGGTTCTTGCTGTGGTTTTGTGTGAAACAGTAACGCTTCGGT
CAGGATATCTTTTACCAGACACCAAAGCATATGGAGATAGAATAGAAAGAATCCTTTGCTCAGTTTGAACATTGACCCTG
ATGCAAAGGTGGAAGAAGAACCCAAAGAAGAACTTGAAGACACAACAGAAGACACAGAGCAAGATGAAGACAAAGAAATG
GATGTAGGAACAGATGAAGAAGAACAAGAAACAGCAAAGGAATCTACAGCTGAAAACGATAAATTG

Alignment

ORF - retro_ptro_170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 56.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDEYKAFYKSFSKESDDPMAYIHFTAEGEVTFKSILFVPTSAPRGLFDEYGSKKSDYIKLYVRRVFITDD
          EDEYKAFYKSFSKESDDPMAYIHFT.EGEVTFKSILFVPTS.PRGLFDEYGSKKSDYIKLYV..VFITD.
Retrocopy EDEYKAFYKSFSKESDDPMAYIHFTTEGEVTFKSILFVPTSDPRGLFDEYGSKKSDYIKLYVLCVFITDE

Parental  FHDMMPKYLNFVKGVVDSDDLPLNVSRETLQQHKLLKVIRKKLVRKTLDMIKKIADDKYNDTFWKEFGTN
          FHD.MPKYLNFVKGVVDSDDLPLNVS.ETLQQHKLLKVIRKKLV.KTLD.IKKIA..KYND.FWKEFGTN
Retrocopy FHDRMPKYLNFVKGVVDSDDLPLNVSLETLQQHKLLKVIRKKLVCKTLDKIKKIAGEKYNDNFWKEFGTN

Parental  IKLGVIEDHSNRTRLAKLLRFQSSHHPTDITSLDQYVERMKEKQDKIYFMAGSSRKEAESSPFVERLLKK
          IKLGVIEDHSN.T.LAKLL.FQSSHHPTDIT.LDQYVERMK.KQDKIYFMAGSSRKEAES.PFVERLLKK
Retrocopy IKLGVIEDHSNQTCLAKLLMFQSSHHPTDITTLDQYVERMKGKQDKIYFMAGSSRKEAESPPFVERLLKK

Parental  GYEVIYLTEPVDEYCIQALPEFDGKRFQNVAKEGVKFDESEKTKESREAVEKEFEPLLNWMKDKALKDKI
          GYEVIYLTEPVDE.CIQA.P.FDGKRFQNV.KEG.KFD.SEKTKES.EAVEKEFEPLLNWMKDKALKDKI
Retrocopy GYEVIYLTEPVDEHCIQAFPKFDGKRFQNVVKEGMKFDKSEKTKESHEAVEKEFEPLLNWMKDKALKDKI

Parental  EKAVVSQRLTESPCALVASQYGWSGNMERIMKAQAYQTGKDISTNYYASQKKTFEINPRHPLIRDMLRRI
          EKAVVSQ.LTES.CALVASQYG.SGN.ERIMKAQAYQT.KD.STNYYASQKKTFEINPRHPLIRDML..I
Retrocopy EKAVVSQHLTESLCALVASQYGRSGNTERIMKAQAYQTSKDSSTNYYASQKKTFEINPRHPLIRDML**I

Parental  KEDEDDKTVLDLAVVLFETATLRSGYLLPDTKAYGDRIERML-RLSLNIDPDAKVEEEPEEEPEETAEDT
          KE.EDDK.VL.LAVVL.ET.TLRSGYLLPDTKAYGDRIER.L..LSLNIDPDAKVEEEP.EE.E.T....
Retrocopy KEGEDDKIVLVLAVVLCETVTLRSGYLLPDTKAYGDRIERIL<LLSLNIDPDAKVEEEPKEELEDT----

Parental  TEDTEQDEDEEMDVGTDEEE-ETAKESTVEKDEL
          TEDTEQDED.EMDVGTDEEE.ETAKEST.E.D.L
Retrocopy TEDTEQDEDKEMDVGTDEEEQETAKESTAENDKL

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	0.00 RPM	160.66 RPM
SRP007412_cerebellum	0.00 RPM	188.28 RPM
SRP007412_heart	0.03 RPM	229.93 RPM
SRP007412_kidney	0.08 RPM	393.24 RPM
SRP007412_liver	0.26 RPM	820.12 RPM
SRP007412_testis	0.21 RPM	460.21 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_170 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_170 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_184
Macaca mulatta	retro_mmul_391

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166598	2 retrocopies	retro_hsap_1530, retro_hsap_184,
Macaca mulatta	ENSMMUG00000023469	1 retrocopy	retro_mmul_391,
Nomascus leucogenys	ENSNLEG00000006510	1 retrocopy	retro_nleu_993,
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,