RetrogeneDB ID: retro_hsap_340

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:247393241..247394561(+)
• Located in intron of: ENSG00000232347

Retrocopy information

• Ensembl ID: ENSG00000214144
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSPA8
• Ensembl ID: ENSG00000109971
• Aliases: HSPA8, HEL-33, HEL-S-72p, HSC54, HSC70, HSC71, HSP71, HSP73, HSPA10, LAP1, NIP71
• Description: heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]

Sequence

>retro_hsap_340
ATGTTGAAGGGAACTGCAGTTGATATTGATATTGGCACCACCTACTCTTGTGTGGGTGTTTTCCAGCACGGGAAAGTAGA
GATAATTGCCAATGATCAGGGAAACCGAACCACTCCAAGCTATGTTGCCTTTACAGACACTGAACGATTGATAGGTGATG
CCACAAAGAATCAAGTTGCAATGAACCCCACCAACATGGTTTTTTGATGCCAAACATCTAATTGGATGCAGATTTGATGA
TGCTGTTGTCCAGCCTGATATGAAGTATTGGCCCTTCATGGTGGTGAATGATGCTGGCAGGCCCAAGGTCCAAGTGGAAT
ACAAGGGAGAGACCAAAAGCTTCTACCCAGAGGAGGTACCCTCTATGGTTCTGACAAAGATGAAGGAAATTGCAGAAGCA
TACCTTGGGAATATGGTTACCAATGCTGTGGTCACAGTGCCAGCTTACTTTAATGACCCTCAGCATCAGGCTACCAAATA
TGCTAGAACTATTGCTGGTCTCAATGTACTTAGAAGTATCAGTGAGCCAACTGTAGCTGCTACTGCTTACAGCTTAGACA
AAAAGGTTGGAGCTGAAAGAAATGTGCTGACCTTTGACCTGAGAGGTGGGACTTTTGATGTGTCAATCCTCACTATTGAG
GATGGAATCTTTGAGGTCAGATCTACAGCTGGAGACACCCACTTGGGTGGAGAAGACTTTGACAACCGAATGTCAACCAT
TTTATTGCTGAGTTCAAGAGCAAGCATAAGAAGGACATCAGTGAGAATAAGAGAGCTGTAAGATGCCTCCATACTGCTTA
TGAACATGCTAAGTGTACTCTCTCTTCCAGCATCCAGGCCAGTATTGGGATCGATTCTCTCTATGAAGGAATAAACTTCT
ATATGTCCATTGCCTGTGCCCGATTTGAAGAATTGAATGCTGACCTGTTCCATAGCACCCTAGACCCCATAGAGAAAGCC
CTTCAAGATGCCAAACTGGACAAGTCAAAGATTCATGATATTGTCCTGTTTGGTGGTTCTACTCATATCCCCAAGATTCA
GAAGCTTCTCCAAGACTTCATCAATGGAAAAGAACCGAATAAGAGCATCAATCCTGATGAAGCTCTTGCTTATGGTGCAG
CTGTTCAGGCAGCCATCCTATCTGGAGACAAGTCTGAAAATGTTCAAGAGTTGCTCCTCTTAGATGTCTCTCCTCTTTCC
CTTGGTATTGAAACTGCTGGTGGAGTCACCACTGTCTTCATCAAGCGTAATACTACCATTCCTACCAAGCAGACACAGAC
CTTCACTACCTATTCTGGCAACCAGCCTGGTGTGCTTATT

Alignment

ORF - retro_hsap_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.78 %
• Parental protein coverage: 68.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVF-D
          M.KG.AV.ID.GTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDA.KNQVAMNPTN.VF.D
Retrocopy MLKGTAVDIDIGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDATKNQVAMNPTNMVF>D

Parental  AKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTV
          AK.LIG.RFDDAVVQ.DMK.WPFMVVNDAGRPKVQVEYKGETKSFYPEEV.SMVLTKMKEIAEAYLG..V
Retrocopy AKHLIGCRFDDAVVQPDMKYWPFMVVNDAGRPKVQVEYKGETKSFYPEEVPSMVLTKMKEIAEAYLGNMV

Parental  TNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSI
          TNAVVTVPAYFND.Q.QATK.A.TIAGLNVLR.I.EPT.AA.AY.LDKKVGAERNVL.FDL.GGTFDVSI
Retrocopy TNAVVTVPAYFNDPQHQATKYARTIAGLNVLRSISEPTVAATAYSLDKKVGAERNVLTFDLRGGTFDVSI

Parental  LTIEDGIFEVKSTAGDTHLGGEDFDNRM-VNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSST
          LTIEDGIFEV.STAGDTHLGGEDFDNRM.VNHFIAEFK.KHKKDISENKRAVR.L.TA.E.AK.TLSSS.
Retrocopy LTIEDGIFEVRSTAGDTHLGGEDFDNRM<VNHFIAEFKSKHKKDISENKRAVRCLHTAYEHAKCTLSSSI

Parental  QASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQK
          QASI.IDSLYEGI.FY.SI..ARFEELNADLF..TLDP.EKAL.DAKLDKS.IHDIVL.GGST.IPKIQK
Retrocopy QASIGIDSLYEGINFYMSIACARFEELNADLFHSTLDPIEKALQDAKLDKSKIHDIVLFGGSTHIPKIQK

Parental  LLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNT
          LLQDF.NGKE.NKSINPDEA.AYGAAVQAAILSGDKSENVQ.LLLLDV.PLSLGIETAGGV.TV.IKRNT
Retrocopy LLQDFINGKEPNKSINPDEALAYGAAVQAAILSGDKSENVQELLLLDVSPLSLGIETAGGVTTVFIKRNT

Parental  TIPTKQTQTFTTYSDNQPGVLI
          TIPTKQTQTFTTYS.NQPGVLI
Retrocopy TIPTKQTQTFTTYSGNQPGVLI

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
bodymap2_adipose	0.00 RPM	378.65 RPM
bodymap2_adrenal	0.00 RPM	331.67 RPM
bodymap2_brain	0.05 RPM	863.93 RPM
bodymap2_breast	0.00 RPM	569.52 RPM
bodymap2_colon	0.00 RPM	1201.80 RPM
bodymap2_heart	0.00 RPM	645.86 RPM
bodymap2_kidney	0.00 RPM	1396.28 RPM
bodymap2_liver	0.00 RPM	656.44 RPM
bodymap2_lung	0.00 RPM	884.51 RPM
bodymap2_lymph_node	0.00 RPM	1648.41 RPM
bodymap2_ovary	0.00 RPM	901.10 RPM
bodymap2_prostate	0.00 RPM	540.08 RPM
bodymap2_skeletal_muscle	0.00 RPM	473.34 RPM
bodymap2_testis	0.00 RPM	864.58 RPM
bodymap2_thyroid	0.00 RPM	1387.20 RPM
bodymap2_white_blood_cells	0.02 RPM	1500.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_340 was not detected

EST

No EST(s) were mapped for retro_hsap_340 retrocopy.

TSS

No TSS is located nearby retro_hsap_340 retrocopy 5' end.

Lab

retro_hsap_340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_340 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_272
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	ENSG00000044574	1 retrocopy	retro_hsap_3005,
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,
Homo sapiens	ENSG00000113013	1 retrocopy	retro_hsap_2214,
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	ENSPTRG00000004404	5 retrocopies	retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
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,