RetrogeneDB ID: retro_pabe_415

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:92935864..92937236(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AB1
• Ensembl ID: ENSPPYG00000016655
• Aliases: None
• Description: heat shock protein HSP 90-beta [Source:RefSeq peptide;Acc:NP_001126444]

Sequence

>retro_pabe_415
GAAGAAGAAAAGAAGGATGGTGACAAAAAGAATAAGAAGATTAAGGAAAAGTACATCGATCAAGAAAAACTCAACAAAAC
AAAGCCCATCTGGACCAGAAATCCTGATGATGTTACTAATGAGGAGTAAGAATTCTACAAGAGCTTGACCAATGACTGGG
AAGATCACTTGGCAGTGAAGCATTTTTCAGTTGAAGGACACTTGGAACTCAGAGCCCTTCTATTTGTCCCACAACATGCT
CCTTTTGACTTGTTTGAAAAGAGAAAGAAAAAGAACAACATCAAATTGTGTGTACAGAGTTTTCATCATGGATAACTGTG
AGGAGCTAATCCCTGCGTATCTGAACTTCATTGGAAAGGTGGTGGACTCAAAGGATCTCTGTCTAAATATTTCCCGTGAG
ATGTTGCGACAAAGCAAAATTTTGAAAGTTATCAGGAAGAATTTGGTCAAAAAATGCTTAGAACTCTTTACCAAACTGGC
AGAAGATAAAGAGAACTACAAGAAGTTCTATGAGCAGTTCTCTAAAAGCATAAAGCTTGAAATATACAAAGACTCTCAAC
ATTGGAAGAAGTTTTCAGAGCTATTAAGATACTACACATCTGCTTCTGGTTGATGAGATGGTTTCTCTGAAGGACTATTG
CACCAGAATGAAGGAAAACTAGAAACATATCTATTACATCACAGGTGAGACCAAGGACCAGGTAGCTAAATTTGTGGAAT
GTCTTTGGAAACATGGCTTAGAAGTGATCTATATGATCAAGTCAATTGATGAGTACTGTGTCCAACACTGAAGGAATTTG
AGGGGAAGACTTCAGTGTCAGTCACCAAAGAGGGCTTGGAACTTCCAGAGGATGAAGAAGAAAAAAAGAAACAGGAAGAG
AAAAAAACAAAGTTTGAGAACATCTGTAAAATCATGAAAGACCTATTGGAGAAAAAAGTTGAAAAGGTGGTTGTGTCAAA
CTGATTGGTGGCGTCTCCATGCTGTATTGTCATGAGCATATATGGCTGGACAGCAAACGTGGAAAGAGTCATGAAAGCTC
AAGCCCTAAGAGACAACTCAACAATGGGTTACATGGCAGCAAAGAAACACGTGGAGATAAACCCTGACCATTCCATTACT
GAGACCTTAAGGCAAAAGGCAGAGGCATATAAGTACAAGTCTGTGTAGGATCTGGTCATCTTGCTTTATGAAACTGCTCT
TTTGTCTTCCGGATTTGGTCTGGAAGATCCCCAGACACATGCTAACAGGATCTACAGGATGATCAAACTTGGTGTGGGTA
TTGATGAAAATGACCCTACTGCTGATGATACTACTGAAGAAATGTCACCCCTTGAAGGAGACAATGACACATCATGCATG
GAAGAAACAGAC

Alignment

ORF - retro_pabe_415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.94 %
• Parental protein coverage: 64.36 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLE
          ....KD..KK.KKIKEKYIDQE.LNKTKPIWTRNPDD.T.EE..EFYKSLTNDWEDHLAVKHFSVEG.LE
Retrocopy EEEKKDGDKKNKKIKEKYIDQEKLNKTKPIWTRNPDDVTNEE*-EFYKSLTNDWEDHLAVKHFSVEGHLE

Parental  FRALLFI-PRRAPFDLFENKKKKNNIKLY-VRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQ
          .RALLF..P....F.L....K.K.......V.RVFIMD.C.ELIP.YLNFI..VVDS.DL.LNISREML.
Retrocopy LRALLFV<PTTCSF*LV*KEKEKEQHQIV<VYRVFIMDNCEELIPAYLNFIGKVVDSKDLCLNISREMLR

Parental  QSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSG-DE
          QSKILKVIRKN.VKKCLELF..LAEDKENYKKFYE.FSK..KL.I..DS......SELLRY.TS.SG.DE
Retrocopy QSKILKVIRKNLVKKCLELFTKLAEDKENYKKFYEQFSKSIKLEIYKDSQHWKKFSELLRYYTSASG>DE

Parental  MTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQ-LKEFDGKSLV
          M.SL..Y..RMKE..K.IYYITGE.K.QVA...FVE...K.G.EV.YM...IDEYCVQ..LKEF.GK..V
Retrocopy MVSLKDYCTRMKEN*KHIYYITGETKDQVAK--FVECLWKHGLEVIYMIKSIDEYCVQH<LKEFEGKTSV

Parental  SVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMER
          SVTKEGLELPED.............FEN.CK.MK..L.KKVEKV..SN.LV.SPCCIV.S.YGWTAN.ER
Retrocopy SVTKEGLELPEDXXXXXXXXXXXXXFENICKIMKDLLEKKVEKVVVSN*LVASPCCIVMSIYGWTANVER

Parental  IMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQ
          .MKAQALRDNSTMGYM.AKKH.EINPDH.I.ETLRQKAEA.K..K.V.DLV.LL.ETALLSSGF.LEDPQ
Retrocopy VMKAQALRDNSTMGYMAAKKHVEINPDHSITETLRQKAEAYKY-KSV*DLVILLYETALLSSGFGLEDPQ

Parental  THSNRIYRMIKLGLGIDEDEVAAEEPSAAVPDEIPPLEGDEDASRMEEVD
          TH.NRIYRMIKLG.GIDE....A.........E..PLEGD.D.S.MEE.D
Retrocopy THANRIYRMIKLGVGIDENDPTADDTT----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	0.06 RPM	1001.09 RPM
SRP007412_cerebellum	0.00 RPM	799.65 RPM
SRP007412_heart	0.00 RPM	514.20 RPM
SRP007412_kidney	0.00 RPM	545.93 RPM
SRP007412_liver	0.00 RPM	429.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_415 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_415 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_237
Pan troglodytes	retro_ptro_207

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
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,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Otolemur garnettii	ENSOGAG00000011961	1 retrocopy	retro_ogar_2574,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pongo abelii	ENSPPYG00000016655	2 retrocopies	retro_pabe_2425, retro_pabe_415 ,
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,