RetrogeneDB ID:

retro_pabe_907

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:12:18045386..18046679(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPPYG00000025948
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_907
ATGGGTCAAAGTCAGAGTGGTGGTCATGGTCCTGGAGGTCAAGAAGGATGATAAGGACAAGAAAAAGAAATACGAACTTC
CAGTACCAACTAGAGTAGGGCAAAAGAAGAAAACAGACCAGATGTTGCCAACAAACTGCCACTGGTGACAACTCACACTC
AGTGCCAGTTAAAATTATTCAAGTTAGAAAGAATTAAAGACTATCTTCTCATGGAGAAAGAATTCATTAGAAATCAGGAA
CAAATAAAACCATTAGAAGAAAAGCAAGAGGAAGAAAGATCAAAAGCGGATGATCTGAGGGGGACCCTGATGTCCGAGGA
ATGTTGGAAGAGATCACCCATGACAACCATGCCATCGTGTCCACATCTGTGGGCTCAGAACATTACATCAGCATTCTTTC
ATTTGTAGACAAGGGCCTGCTGGAACCTGGCTTGGTCCTGCTCAACCACAACGTTCATGCCATGATAGGGGTGCTGATGG
ATGACACGGATCCCCTGGTCACAGTGATGAAGGTGGAAAAGGCCCCCCAGGAGACCTATGCCAATACTGGAGGATTGGAA
ACCAAATTCAGGAAATTAAGGAATCTGGAATCTGTGGAGCTTCCTCTCACCTATTCTGAATACTATGAAGAAATGGGTAT
GAAGCCTCCTCAAGGGGGTCATTCTCTATGGTCCACTGGGCACAGGCAAAACTTTGTTAGTCAAAGCAGCAGCAAACCAA
ACCCCAGCCACTTTCTTGAGAGTGGTTGGCTCTGAACTTATTCAGAAGTACCTAGGTGATGGGCTCAAACCCACGCTGGA
ATTGTTTCGAGTTGCTGAAGAACATGCACCATTCATCATGTTTATTGATGAAATTGATGCCATTGGTTCAAAAAGATACA
ACTCAAATTCTGGTGGTGAGAGAGAAATTCAGTGAACAATGTTGAAACTGTTGAATCAGTTGGATGGATTTGATTCTAGG
GGAGATGTGAAAGCTATCATGGCCACAAACCAAATAGAAACTTTGGATCCCGCACTTATCAGACCAGGCTGCATTGACAG
GAAGATCGAGGTCCCCCTGCCCGATGAAAAGAATGAGAAGCACATCATTCAGATTCACACTAGCAGGATGAGGGTGGCCG
ATGATGTAACCCTGCATGACTTGATCATGGCTAAAGATGACCTCTCTGGTGATGACATCAAGGCAATCTGTACAAAAGCT
GGTCTGAAGGCCTTAAGAGAACTTAGAATAAAAGTAACAAATGAAGACTTCAAAAAATCGAAAGAAAATGTTCTTTATAA
GAAACAGGAAGGG

ORF - retro_pabe_907 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.18 %
Parental protein coverage: 98.41 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGQSQSGGHGPGGG-KKDDKDKKKKYEPPVPTRVGKKKKKTKG-PDAASKLPLVTPHTQCRLKLLKLERI
MGQSQSGGHGP.GG.KKDD..K.KK.....P.......KK....PD.A.KLPLVT.HTQC.LKL.KLERI
RetrocopyMGQSQSGGHGP-GG>KKDD--KDKKKKYELPVPTRVGQKKKTD<PDVANKLPLVTTHTQCQLKLFKLERI
ParentalKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSV-GTLEEIIDDNHAIVSTSVGSEHYVSILS
KDYLLME.EFIRNQEQ.KPLEEKQEEERSK.DDLRGT.MS..G.LEEI..DNHAIVSTSVGSEHY.SILS
RetrocopyKDYLLMEKEFIRNQEQIKPLEEKQEEERSKADDLRGTLMSE<GMLEEITHDNHAIVSTSVGSEHYISILS
ParentalFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIK--ESVELPL
FVDK.LLEPG..VLLNH.VHA.IGVLMDDTDPLVTVMKVEKAPQETYA..GGL..........ESVELPL
RetrocopyFVDKGLLEPGL-VLLNHNVHAMIGVLMDDTDPLVTVMKVEKAPQETYANTGGLETKFRKLRNLESVELPL
ParentalTHPEYYEEMGIKPP-KGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVA
T..EYYEEMG.KPP.KGVILYGP.GTGKTLL.KA.ANQT.ATFLRVVGSELIQKYLGDG.K...ELFRVA
RetrocopyTYSEYYEEMGMKPP>KGVILYGPLGTGKTLLVKAAANQTPATFLRVVGSELIQKYLGDGLKPTLELFRVA
ParentalEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRP
EEHAP.I.FIDEIDAIG.KRY.SNSGGEREIQ.TML.LLNQLDGFDSRGDVK.IMATN.IETLDPALIRP
RetrocopyEEHAPFIMFIDEIDAIGSKRYNSNSGGEREIQ*TMLKLLNQLDGFDSRGDVKAIMATNQIETLDPALIRP
ParentalGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKV
G.IDRKIE.PLPDEK..K.I.QIHTSRM..ADDVTL.DLIMAKDDLSG.DIKAICT.AGL.ALRE.R.KV
RetrocopyGCIDRKIEVPLPDEKNEKHIIQIHTSRMRVADDVTLHDLIMAKDDLSGDDIKAICTKAGLKALRELRIKV
ParentalTNEDFKKSKENVLYKKQEG
TNEDFKKSKENVLYKKQEG
RetrocopyTNEDFKKSKENVLYKKQEG

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 52 .80 RPM
SRP007412_cerebellum 0 .00 RPM 42 .93 RPM
SRP007412_heart 0 .00 RPM 32 .33 RPM
SRP007412_kidney 0 .03 RPM 37 .82 RPM
SRP007412_liver 0 .00 RPM 34 .70 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_907 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_907 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_907 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1090
Pan troglodytes retro_ptro_742
Gorilla gorilla retro_ggor_858
Parental genes homology:
Parental genes homology involve 25 parental genes, and 101 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000018394 retrocopies
retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris ENSCAFG000000175102 retrocopies
retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni ENSCHOG000000135951 retrocopy
retro_chof_1954,
Callithrix jacchus ENSCJAG000000177017 retrocopies
retro_cjac_1152, retro_cjac_1537, retro_cjac_2417, retro_cjac_2433, retro_cjac_4219, retro_cjac_661, retro_cjac_678,
Cavia porcellus ENSCPOG000000024241 retrocopy
retro_cpor_144,
Dasypus novemcinctus ENSDNOG000000064581 retrocopy
retro_dnov_2162,
Equus caballus ENSECAG000000036011 retrocopy
retro_ecab_355,
Echinops telfairi ENSETEG000000026611 retrocopy
retro_etel_580,
Felis catus ENSFCAG000000113108 retrocopies
retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Homo sapiens ENSG0000010076410 retrocopies
retro_hsap_1090, retro_hsap_1278, retro_hsap_2080, retro_hsap_2658, retro_hsap_2810, retro_hsap_2873, retro_hsap_3323, retro_hsap_3416, retro_hsap_3793, retro_hsap_975,
Gorilla gorilla ENSGGOG000000106208 retrocopies
retro_ggor_1004, retro_ggor_1298, retro_ggor_1629, retro_ggor_1954, retro_ggor_1993, retro_ggor_2309, retro_ggor_780, retro_ggor_858,
Macropus eugenii ENSMEUG000000015261 retrocopy
retro_meug_623,
Microcebus murinus ENSMICG000000167337 retrocopies
retro_mmur_1039, retro_mmur_1063, retro_mmur_1245, retro_mmur_1577, retro_mmur_216, retro_mmur_839, retro_mmur_983,
Myotis lucifugus ENSMLUG000000074712 retrocopies
retro_mluc_2490, retro_mluc_508,
Macaca mulatta ENSMMUG000000229901 retrocopy
retro_mmul_255,
Mustela putorius furoENSMPUG000000081504 retrocopies
retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus ENSMUSG000000211783 retrocopies
retro_mmus_1517, retro_mmus_1826, retro_mmus_812,
Nomascus leucogenys ENSNLEG0000001701310 retrocopies
retro_nleu_1123, retro_nleu_1163, retro_nleu_1589, retro_nleu_1625, retro_nleu_1669, retro_nleu_2318, retro_nleu_2625, retro_nleu_429, retro_nleu_616, retro_nleu_706,
Oryctolagus cuniculus ENSOCUG000000062314 retrocopies
retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii ENSOGAG000000323432 retrocopies
retro_ogar_3014, retro_ogar_367,
Pongo abelii ENSPPYG00000025948 9 retrocopies
retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907 ,
Pan troglodytes ENSPTRG000000066239 retrocopies
retro_ptro_1530, retro_ptro_1904, retro_ptro_1944, retro_ptro_2153, retro_ptro_2321, retro_ptro_2573, retro_ptro_672, retro_ptro_742, retro_ptro_874,
Pteropus vampyrus ENSPVAG000000100203 retrocopies
retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Ictidomys tridecemlineatus ENSSTOG000000016551 retrocopy
retro_itri_780,
Tursiops truncatus ENSTTRG000000135821 retrocopy
retro_ttru_239,


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