RetrogeneDB ID:

retro_pabe_794

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:11:104029167..104030381(-)
Located in intron of:ENSPPYG00000003833
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DKFZP459C0539
Ensembl ID:ENSPPYG00000008456
Aliases:None
Description:DKFZP459C0539 protein [Source:RefSeq peptide;Acc:NP_001128829]


Retrocopy-Parental alignment summary:






>retro_pabe_794
GAAAGACCATCTTATGCCCCACCTCCCACCCCAGCTCCTACAACACAAATGCCCAGCACACCAAGGTTTGTGGGATACAG
TCCATACAGTCATCTCGCCTACAACAATTACAGGCTGGGAGGGAACCCTGGTACCAACAGCCAGTTCACGGCATCCTCTG
GTGCTACGATTCCAAAACCCCCAAAGCCACCAGATAAGCTGCTGATGCCCTACATGAGGTACAGCTGAAAGGTCTGGGAC
CAAAGTAAGGGCTTCCAACCCAGACCTAAAGTTGTGGAAGACTGGCAAGATTATTGGTGGCATGTGGCGAGATCTCACTG
ATGAAGAAAAACAAGAATATTTAAATGGATACGAAGCAGAAAGTTAGAGTACAATGAATTTATGAAGGCCTATCATAATT
CCCCCACCTACCTTGCTTACGTAAATGCAAAAAATCGTGCAGAAGCTGCTTTAGAGGAAGAAAGTTGACAGAGACAGTCT
CACATGGAGAAAGGAGAACTATATATGAGCATTCAGCTCTGCTGAAGATCCAGATGATTATGATGATGGGTTTTTAGTGA
AGCATACAGCCACTGACTGTTTCCAGAGAAACCGTCACCTCTTCAGTGAAATCCTTAGTGAGAGTGTGGTGCCAGACGTT
CGGTCAGTTGTCGCAACAGCTAGAATGCAGGTCCTTAAATGACAGGTTCAGTCCTTAATGGTTCCTCAGCGAAAACTAGA
AGCTGAACTTCTTCAAATACAGGAGGAGAAGAGGAAATTCCTAGAAAGCACAGATTCACTTAACAATGAACTTAAAAGGT
TGTGCGGTCTGACAGTAGAAGTGGATATGGAGAGAGTTGCAGCTGAGATTGCACAGGCAGAGGAACAGACTGGCAAAAAG
CAGGAGGAAAGGGAGAAGGAGGCAGCAGAGCAAGCCGAGTGCAGTCAAAGCAGCATCATTCGTGAGGAAGAACAAGCACC
AAACAAAGGTGAGGAGAAGAAAGACGAGGAGAACATTCCAATGGAGACAGAGGAGACACACCTTGAAGAAACCACAGAGT
CAACAGAATGGTGAAGAAGGCACGTCTACTACTGAGGACAAGGAGAGTGGGCAGGAGGGGGTTGACAGTATGGCAGAGGA
AGGAACCAGTGATAGTAACACTGGCTCAGAGAGCAACAGCACAACAGTGGAAGAGCCACTGACAGATCCCCTACCAGAAG
ATGAGAAAAAAGAA

ORF - retro_pabe_794 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.5 %
Parental protein coverage: 99.51 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNPGTNSRVTASSGITIPKPPKPPDKPLMP
.RPSYAPPPTPAP.TQMPSTP.FVGY.PYSHLAYNNYRLGGNPGTNS..TASSG.TIPKPPKPPDK.LMP
RetrocopyERPSYAPPPTPAPTTQMPSTPRFVGYSPYSHLAYNNYRLGGNPGTNSQFTASSGATIPKPPKPPDKLLMP
ParentalYMRYSRKVWDQ-VKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAE-KIEYNESMKAYHNSPAYL
YMRYS.KVWDQ.V.ASNPDLKLW..GKIIGGMWRDLTDEEKQEYLN.YEAE.K.EYNE.MKAYHNSP.YL
RetrocopyYMRYS*KVWDQ>VRASNPDLKLWKTGKIIGGMWRDLTDEEKQEYLNGYEAE<KLEYNEFMKAYHNSPTYL
ParentalAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQ-PAEDPDDYDDGFSMKHTATARFQRNHRLISEILSE
AY.NAK.RAEAALEEES.QRQS.MEKGE.YMSIQ..AEDPDDYDDGF..KHTAT..FQRN..L.SEILSE
RetrocopyAYVNAKNRAEAALEEES*QRQSHMEKGELYMSIQ>SAEDPDDYDDGFLVKHTATDCFQRNRHLFSEILSE
ParentalSVVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVE
SVVPDVRSVV.TARMQVLK.QVQSLMV.QRKLEAELLQI....QE.KRKFLESTDS.NNELKRLCGL.VE
RetrocopySVVPDVRSVVATARMQVLK*QVQSLMVPQRKLEAELLQI----QEEKRKFLESTDSLNNELKRLCGLTVE
ParentalVDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQSSIVPEEEQAANKGEEKKDDENIPMETEETHLEE
VDME..AAEIAQAEEQ..K.QEEREKEAAEQAE.SQSSI..EEEQA.NKGEEKKD.ENIPMETEETHLEE
RetrocopyVDMERVAAEIAQAEEQTGKKQEEREKEAAEQAECSQSSIIREEEQAPNKGEEKKDEENIPMETEETHLEE
ParentalTTES-QQNGEEGTSTPEDKESGQEGVDSMAEEGTSDSNTGSESNSATVEEPPTDPIPEDEKKE
TTES.Q...E....T.EDKESGQEGVDSMAEEGTSDSNTGSESNS.TVEEP.TDP.PEDEKKE
RetrocopyTTES>QNGEEGTSTT-EDKESGQEGVDSMAEEGTSDSNTGSESNSTTVEEPLTDPLPEDEKKE

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 .11 RPM 50 .65 RPM
SRP007412_cerebellum 0 .00 RPM 64 .81 RPM
SRP007412_heart 0 .03 RPM 22 .85 RPM
SRP007412_kidney 0 .10 RPM 52 .07 RPM
SRP007412_liver 0 .03 RPM 29 .32 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_794 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_794 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_794 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_922
Pan troglodytes retro_ptro_639
Parental genes homology:
Parental genes homology involve 21 parental genes, and 82 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000160258 retrocopies
retro_cfam_1057, retro_cfam_1131, retro_cfam_1134, retro_cfam_1300, retro_cfam_1412, retro_cfam_1803, retro_cfam_2063, retro_cfam_2127,
Choloepus hoffmanni ENSCHOG000000087273 retrocopies
retro_chof_1245, retro_chof_482, retro_chof_573,
Callithrix jacchus ENSCJAG000000135734 retrocopies
retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Felis catus ENSFCAG000000096462 retrocopies
retro_fcat_234, retro_fcat_513,
Homo sapiens ENSG000000735845 retrocopies
retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla ENSGGOG000000118032 retrocopies
retro_ggor_1020, retro_ggor_931,
Microcebus murinus ENSMICG000000098214 retrocopies
retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus ENSMLUG000000046091 retrocopy
retro_mluc_1209,
Macaca mulatta ENSMMUG000000040053 retrocopies
retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furoENSMPUG000000146604 retrocopies
retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus ENSMUSG000000379355 retrocopies
retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys ENSNLEG000000019574 retrocopies
retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus ENSOCUG000000089811 retrocopy
retro_ocun_59,
Otolemur garnettii ENSOGAG000000016527 retrocopies
retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps ENSOPRG000000009851 retrocopy
retro_opri_731,
Pongo abelii ENSPPYG00000008456 4 retrocopies
retro_pabe_2973, retro_pabe_3251, retro_pabe_794 , retro_pabe_994,
Pan troglodytes ENSPTRG000000229025 retrocopies
retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus ENSPVAG000000113551 retrocopy
retro_pvam_237,
Rattus norvegicus ENSRNOG000000106767 retrocopies
retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri ENSTBEG0000000077010 retrocopies
retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,
Tursiops truncatus ENSTTRG000000138851 retrocopy
retro_ttru_1217,


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