RetrogeneDB ID: retro_pabe_2193

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b_random:7842828..7844216(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459D1928
• Ensembl ID: ENSPPYG00000003987
• Aliases: HSPA8, HSC70
• Description: heat shock cognate 71 kDa protein [Source:RefSeq peptide;Acc:NP_001125783]

Sequence

>retro_pabe_2193
CATCTTGGGAAGACTATTTCCAGTGTTATGGTCATAGGGCCTAATGACTCTAATGTCAAGCTAACAAAGATCCTGAAACC
ATTGCTGGTCTCAATGTACTTAGAATTATCAATGAGCCAACTGCTGCTTCTATTGCTATGGCACAGACAAAAAGGTTGAA
GCTGAAAGACGTGTGCTCATCTATGACTTAAGATATGAAATTTTTGATGTGTCTGTCCTCACTCTTGAGGATGAAATCTT
TGAGATCAAATTTACAGCTGGAGACACCCACTTAGGTGAAGAAGATTTTGACAACCAAATGATCAACCATTTTATTGCTG
AGTTCAAATACAAGCATAAGGACAGTAGTGAGAACAACAGGGCTGTCTGATGCTTCTGTACTGCTTGTGATGGGCTAATT
GCACTCTCCCTTCCAGCACCCAGGCCAGTAGTGAGATTAATTCCCTCTGTGATGGAACAGATATTTATACCTCCATTACC
CATGCCCAATTTGAAGAACTGAATGCTGTCCTGTTCCGTGGCACCCAGGACCCCATAGAGATAGCCCTTCAGGACACCAA
ACTAGGCAAGTTGCAGATCCATGTTATTGTCCTGGTAGGTGGTTCTATCTTTATCTCCTAGATCCAAAAGCTCCCTCAAT
AATTATTTAGTGGAAAAGAACTGAGCAAGAGCATTGACCCTGATAAAGCTGTTGTTTATGCTGCAGCAGTCCAGGCAGCC
ATCCTATCTTAAGACAAATCTTAAACTGTTCAAGATTTGCTACTTTTGGATTCACTCCTCTTCTCTTTGGTAATGATGCT
GCTGTGGAGTCATGACTGTTCCCATGAAATGCAATATACTTTTCTTACCAAGCAGATCCAGACCTTCACTACCTACCCTG
ACAACCAACCTGATGTCCTCATTCAAGTTTATGAAGGTGAGAGTGCCATAACCAAGGATAACAATTTGCTTGCTATCCAG
GGCAAGTTTGAGCTCACAGGCATACTTCCTGCTCCCTTTGCTGTTCCTCAAATTAAAGTCACTTGTGATAGTGATGTTAA
TAGCAGCCTCAATATCTCTGCTATAGGTAAGAGTACAGAAAAAGAGAACAAATTATCATCACTAATGACCAGGGGCATTT
GAGCATGGAAGACATTGAGAATATGGTCCAGGAAGCTGAGTACAAAGCTGAAGATGAGAAGCAGAAGGACAAGGTGGCAT
CAAAGAATTCACCTGACTCTTATGCATTCAACATGAAAGCAACTGAGAAACTTCAAGGCAAGATCAACAATAAGGATAAA
CAGAAGATTCTTGACAAGTGTAATAAAATCATCAACTGACTTGGTAAGAATCGGACTATAATGAAGGAAGAATTTGAACA
TCAGCAGAAAGAGCTAGTTTGCAGTCCA

Alignment

ORF - retro_pabe_2193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.12 %
• Parental protein coverage: 73.07 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  YLGKTVTNAVVTVPAYFNDSQR-QATKDAGTIAGLNVLRIINEPTAAAIA-YGLDKKVGAERNVLIFDLG
          .LGKT.....V..P...NDS...QA.KD..TIAGLNVLRIINEPTAA.IA.YG.DKKV.AER.VLI.DL.
Retrocopy HLGKTISSVMVIGP---NDSNV<QANKDPETIAGLNVLRIINEPTAASIA<YGTDKKVEAERRVLIYDLR

Parental  GGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACER-A
          ...FDVS.LT.ED.IFE.K.TAGDTHLG.EDFDN.M.NHFIAEFK.KHK.D.SEN.RAV....TAC...A
Retrocopy YEIFDVSVLTLEDEIFEIKFTAGDTHLGEEDFDNQMINHFIAEFKYKHK-DSSENNRAV*CFCTACDG<A

Parental  KRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGS
          ..TL.SSTQAS.EI.SL..G.D.YTSIT.A.FEELNA.LFRGT.DP.E.AL.D.KL.K.QIH.IVLVGGS
Retrocopy NCTLPSSTQASSEINSLCDGTDIYTSITHAQFEELNAVLFRGTQDPIEIALQDTKLGKLQIHVIVLVGGS

Parental  TRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLD-VTPLSLGIETA-GG
          ..I..IQKL.Q..F.GKEL.KSI.PD.AV.Y.AAVQAAILS.DKS..VQDLLLLD..TPL..G...A..G
Retrocopy IFIS*IQKLPQ*LFSGKELSKSIDPDKAVVYAAAVQAAILS*DKS*TVQDLLLLD<FTPLLFGNDAA<CG

Parental  VMTVLIKRNT-TIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLL---GKFELTGIPPAPRGVPQI
          VMTV..K.N..T..TKQ.QTFTTY.DNQP.VLIQVYEGE.A.TKDNNLL...GKFELTGI.PAP..VPQI
Retrocopy VMTVPMKCNI<TFLTKQIQTFTTYPDNQPDVLIQVYEGESAITKDNNLLAIQGKFELTGILPAPFAVPQI

Parental  EVTFDIDANGILNVSAVDKSTGKENK-ITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLE
          .VT.D.D.N..LN.SA..KST.KENK.I.ITND.G.LS.EDIE.MVQEAE.YKAEDEKQ.DKV.SKNS..
Retrocopy KVTCDSDVNSSLNISAIGKSTEKENK<IIITNDQGHLSMEDIENMVQEAE-YKAEDEKQKDKVASKNSPD

Parental  SYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNP
          SYAFNMKAT...EKLQGKIN..DKQKILDKCN.IIN.L.KN.T..KEEFEHQQKEL..VC.P
Retrocopy SYAFNMKAT---EKLQGKINNKDKQKILDKCNKIIN*LGKNRTIMKEEFEHQQKEL--VCSP

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	425.19 RPM
SRP007412_cerebellum	0.00 RPM	531.03 RPM
SRP007412_heart	0.00 RPM	192.27 RPM
SRP007412_kidney	0.00 RPM	310.15 RPM
SRP007412_liver	0.03 RPM	196.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2193 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2193 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca	ENSAMEG00000008425	1 retrocopy	retro_amel_126,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Bos taurus	ENSBTAG00000013162	1 retrocopy	retro_btau_354,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
Callithrix jacchus	ENSCJAG00000007648	5 retrocopies	retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Felis catus	ENSFCAG00000001132	6 retrocopies	retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Gorilla gorilla	ENSGGOG00000008381	8 retrocopies	retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus	ENSMUSG00000015656	8 retrocopies	retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Oryctolagus cuniculus	ENSOCUG00000015533	4 retrocopies	retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pongo abelii	ENSPPYG00000003987	9 retrocopies	retro_pabe_183, retro_pabe_2193 , retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pongo abelii	ENSPPYG00000019609	1 retrocopy	retro_pabe_2491,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Tursiops truncatus	ENSTTRG00000011139	6 retrocopies	retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,