RetrogeneDB ID:

retro_pabe_2254

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:127530705..127532012(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DKFZP459D1928
Ensembl ID:ENSPPYG00000003987
Aliases:HSPA8, HSC70
Description:heat shock cognate 71 kDa protein [Source:RefSeq peptide;Acc:NP_001125783]


Retrocopy-Parental alignment summary:






>retro_pabe_2254
GGAAGTGGCACTTGTAATGCGTCAGTCCTCACTGTTGAGGATGGAATCTTTGAGGTGAAATCTACAGCAGGAGACACCCA
CTTAGGTGGAAAAGACTTTGACAAACCAAGTGGTTCACCATTTTATTGCCGAGTTCAAGCACAAGCATACAAAGGACATC
AGTGAGAATAAGAGAGCTGTCTGACATCCCCATACTGCTTGTGAACGTGCTAATTACACTCTTTCTTGAGCAACCAGGCT
AGTATTGAGATCCATTTTCTCTATGAAGGAATCAATGTCTATACCTCTTACCCATGCCCGATTTGAAGAACTGAATGCTG
ACCTGTTCTGTGACACCTGGACCCCGTAGAGAAAGCTCTTCAAGACGCCAAACTAGACAAGTCACAGATTCATGATATTT
TCCTGGATGGTGGTTCTACTTTTATCCCCAGGATTCAGAAGCTTCTCCAAGACTTTTTCAATGGAAAAGAACTGAATAAG
AGCATCAGCCCTAATGAAGCTGTTGCTTATGGTGCAGCTGTCCAAGCAGCCATTCTGTCTGGCAACAAATCTGAAAATGC
TCAAGATTTGTTGCTCTTGTATGTCATTCTTCCTTCCCATGGTATTGAAACTGATGGTGTAGTCATGACTATTCTCATTA
AGCATAATACTACCATTCCTTCCAAGCAGACAGACCTTCACTATCTACCCTGACAAGCAGCCTGATGTGCTTATTCAGGT
TTATGAAGGTGAGCATGTCATGACCAAGGATACCAACCTGCTTGGCAAGTTTCAGCTCACAGGCATACCTTTGGCACTCC
AAGGTGTTCCTCACATTGAAGTCACATTTGATATTGATGCCAATGGCATCTTCAATGTCTCTGCTGTGCACAAGAGTACA
GGAAAAAGAACAAGGTTACTGTCACTAATGACGAGAGCCATTTTAGCAAGAAAGACATTAAATGTATGGTCCAGGAGGCT
GAGCATTACAAAGCTGAAGATGAGAAGCAGAGACAGATGTCATCCAAGAATTCCCTTTAATCCTATGAATTCAACATGGA
AGCAACTGTTGAAGATGAGAAACTTCAAGGCAAGATTCATGATGAAGACAAACAGAAGATTCTTGTCAGGCGTAATGAAA
TTATTAACTGGATAGATAAGAATCAGGCTGTTGAGAAGGAAGAATTTGAACATCAGCAGAAAGAGCTGGAGAGAGTCTGC
AATCCCATCATTACAAAGCTGTAGCAGAGTGCAGAGGAATGCCTAGGGGATTCACTGTTGGTGGATCTCCTCCCTCTGGT
GGTGCTTTCTCAGGGCCCACCACTGAA

ORF - retro_pabe_2254 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.71 %
Parental protein coverage: 68.58 %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFD-NRMVNHFIAEFKRKHKKDISENKRAVRRLRTACER
G.GT...S.LT.EDGIFEVKSTAGDTHLGG.DFD.N..V.HFIAEFK.KH.KDISENKRAV....TACER
RetrocopyGSGTCNASVLTVEDGIFEVKSTAGDTHLGGKDFD>NQVVHHFIAEFKHKHTKDISENKRAV*HPHTACER
ParentalAKRTLSSSTQASIE-IDSLYEGIDFYTSITRARFEELNADLFRGT-LDPVEKALRDAKLDKSQIHDIVLV
A..TLS..T......I.S..E........T.ARFEELNADLF..T.LDPVEKAL.DAKLDKSQIHDI.L.
RetrocopyANYTLS*ATRLVLRSIFSMKESMSI--PLTHARFEELNADLFCDT<LDPVEKALQDAKLDKSQIHDIFLD
ParentalGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAG
GGST.IP.IQKLLQDFFNGKELNKSI.P.EAVAYGAAVQAAILSG.KSEN.QDLLLL.V...S.GIET..
RetrocopyGGSTFIPRIQKLLQDFFNGKELNKSISPNEAVAYGAAVQAAILSGNKSENAQDLLLLYVILPSHGIET-D
ParentalGVMTVLIKRNTTIPTKQT-QTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEV
GV.........T.......QTFT.Y.D.QP.VLIQVYEGE..MTKD.NLLGKF.LTGIP.A..GVP.IEV
RetrocopyGVVMTILIKHNTTIPSKQ>QTFTIYPDKQPDVLIQVYEGEHVMTKDTNLLGKFQLTGIPLALQGVPHIEV
ParentalTFDIDANGILNVSAVDKSTGK-ENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESY
TFDIDANGI.NVSAV.KSTGK..NK.T.TND....SK.DI..MVQEAE.YKAEDEKQR...SSKNSL.SY
RetrocopyTFDIDANGIFNVSAVHKSTGK<KNKVTVTNDESHFSKKDIKCMVQEAEHYKAEDEKQR-QMSSKNSL*SY
ParentalAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSA-
.FNM.ATVEDEKLQGKI.DEDKQKIL...NEIINW.DKNQ..EKEEFEHQQKELE.VCNPIITKL.QSA.
RetrocopyEFNMEATVEDEKLQGKIHDEDKQKILVRRNEIINWIDKNQAVEKEEFEHQQKELERVCNPIITKL*QSA<
ParentalGGMPGGMPGGFPGGGAPPSGGASSGPTIE
.GMP.G....F..GG.PPSGGA.SGPT.E
RetrocopyRGMPRG----FTVGGSPPSGGAFSGPTTE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_2254 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2254 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2254 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2758
Gorilla gorilla retro_ggor_1918
Parental genes homology:
Parental genes homology involve 29 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Callithrix jacchus ENSCJAG000000076485 retrocopies
retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Gorilla gorilla ENSGGOG000000083818 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 ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 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 ENSMUSG000000156568 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 ENSOCUG000000155334 retrocopies
retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 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 ENSPPYG000000196091 retrocopy
retro_pabe_2491,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,


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