RetrogeneDB ID: retro_ptro_272

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:226713075..226714380(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA8
• Ensembl ID: ENSPTRG00000004404
• Aliases: None
• Description: heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]

Sequence

>retro_ptro_272
GCAGTTGATATTGATATTGGCACCACCTACTCTTGTGTGGGTGTTTTCCAGCACGGGAAAGTAGAGATAATTGCCAATGA
TCAGGGAAACCGAACCACTCCAAGCTATGTTGCCTTTACAGACACTGAACGATTGATCGGTGATGGCACAAAGAATCAAG
TTGCAATGAACCCCACCAACATGGTTTTTTGATGCCAAACATCTAATTGGATGGAGATTTGATGATGCTGTTGTCCAGCC
TGATATGAAGTATTGGCCCTTCATGGTGGTGAATGATGCTGGCAGGCCCAAGGTCCAAGTGGAATACAAGGGAGAGACCA
AAAGCTTCTACCCAGAGGAGGTACCCTCTATGGTTCTGACAAAGATAAAGGAAATTGCAGAAGCATACCTTGGGAATACA
GTTACCAATGCTGTGGTCACAGTGCCAGCTTACTTTAATGACCCTCAGCATCAGGCTACCAAATATGCTAGAACTATTGC
TGGTCTCAATGTACTTAGAATTATCAGTGAGCCAACTGCAGCTGCTACTGCTTACAGCTTAGACAAAAAGGTTGGAGCTG
AAAGAAAAGTGCTGACCTTTGACCTGAGAGGTGGGACTTTTGATGTGCCAATCCTCACTATTGAGGATGGAATCTTTGAG
GTCAAATCTACAGCTGGAGACACCCACTTGGGTGGAGAAGACTTTGACAACCGAATGTCAACCATTTTATTGCTGAGTTC
AAGAGCAAGCATAAGAAGGACATCAGTGAGAACAAGAGAGCTGTAAGATGCCTCCATACTGCTTATGAACATGCTAAGCG
TACTCTCTCTTCCAGCGTCCAGGCCAGTATTGGGATCGATTCTCTCTATGAAGGAATAAACTTCTATATGTCCAGTGCCT
GTGCCCGATTTGAAGAATTGAATGCTGACCTGTTCTATAGCACCCTAGACCCCATAGAGAAAGCCCTTCAAGATGCCAAA
CTGGACAAGTCAAAGATTCATGATATTGTCCTGTTTGGTTGTTCTACTCATATCCCCAAGATTCAGAAGCTTCTCCAAGA
CTTCATCAATGGAAAAGAACTGAATAAGAGCATCAATCCTGATGAAGCTCTTGCTTATGGTGCAGCTGTTCAGGCAGCCA
TCCTATCTGGAGACAAGTCTGAAAATGTTCAAGAGTTGCTGCTCTTAGATGTCTCTCCTCTTTCCCTTGGTATTGAAACT
GCTGGTGGAGTCACCACTGTCTTCATCAAGCATAATACTACCATTCCTACTAAGCAGACACAGACCTTCACTACCTATTC
TGGCAACCAGCCTGGTGTGCTTATT

Alignment

ORF - retro_ptro_272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.41 %
• Parental protein coverage: 68.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVF-DAKRLI
          AV.ID.GTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGD..KNQVAMNPTN.VF.DAK.LI
Retrocopy AVDIDIGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDGTKNQVAMNPTNMVF>DAKHLI

Parental  GRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLG-TVTNAVV
          G.RFDDAVVQ.DMK.WPFMVVNDAGRPKVQVEYKGETKSFYPEEV.SMVLTK.KEIAEAYLG.TVTNAVV
Retrocopy GWRFDDAVVQPDMKYWPFMVVNDAGRPKVQVEYKGETKSFYPEEVPSMVLTKIKEIAEAYLGNTVTNAVV

Parental  TVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDWQVGAERNVLIFDLGGGTFDVSILTIED
          TVPAYFND.Q.QATK.A.TIAGLNVLRII.EPTAAA.AY.LD..VGAER.VL.FDL.GGTFDV.ILTIED
Retrocopy TVPAYFNDPQHQATKYARTIAGLNVLRIISEPTAAATAYSLDKKVGAERKVLTFDLRGGTFDVPILTIED

Parental  GIFEVKSTAGDTHLGGEDFDNRM-VNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIE
          GIFEVKSTAGDTHLGGEDFDNRM.VNHFIAEFK.KHKKDISENKRAVR.L.TA.E.AKRTLSSS.QASI.
Retrocopy GIFEVKSTAGDTHLGGEDFDNRM<VNHFIAEFKSKHKKDISENKRAVRCLHTAYEHAKRTLSSSVQASIG

Parental  IDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDF
          IDSLYEGI.FY.S...ARFEELNADLF..TLDP.EKAL.DAKLDKS.IHDIVL.G.ST.IPKIQKLLQDF
Retrocopy IDSLYEGINFYMSSACARFEELNADLFYSTLDPIEKALQDAKLDKSKIHDIVLFGCSTHIPKIQKLLQDF

Parental  FNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTTIPTK
          .NGKELNKSINPDEA.AYGAAVQAAILSGDKSENVQ.LLLLDV.PLSLGIETAGGV.TV.IK.NTTIPTK
Retrocopy INGKELNKSINPDEALAYGAAVQAAILSGDKSENVQELLLLDVSPLSLGIETAGGVTTVFIKHNTTIPTK

Parental  QTQTFTTYSDNQPGVLI
          QTQTFTTYS.NQPGVLI
Retrocopy QTQTFTTYSGNQPGVLI

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	0.04 RPM	845.51 RPM
SRP007412_cerebellum	0.11 RPM	738.30 RPM
SRP007412_heart	0.00 RPM	709.86 RPM
SRP007412_kidney	0.00 RPM	971.90 RPM
SRP007412_liver	0.00 RPM	502.96 RPM
SRP007412_testis	0.11 RPM	445.77 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_272 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_272 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_340
Gorilla gorilla	retro_ggor_360
Pongo abelii	retro_pabe_355
Macaca mulatta	retro_mmul_580

---

Parental genes homology:

Parental genes homology involve 29 parental genes, and 76 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,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Dipodomys ordii	ENSDORG00000015467	1 retrocopy	retro_dord_16,
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,
Homo sapiens	ENSG00000109971	8 retrocopies	retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
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,
Macaca mulatta	ENSMMUG00000004696	7 retrocopies	retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
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,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Pan troglodytes	ENSPTRG00000000563	1 retrocopy	retro_ptro_2033,
Pan troglodytes	ENSPTRG00000004404	5 retrocopies	retro_ptro_1743, retro_ptro_2507, retro_ptro_272 , retro_ptro_3259, retro_ptro_3264,
Pan troglodytes	ENSPTRG00000017290	1 retrocopy	retro_ptro_1680,
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,