RetrogeneDB ID:

retro_pabe_2737

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:57570875..57572192(-)
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_2737
ATGGGTCAAAGTCAGGGTGGTGGTCATGGTCCTAGACGTGGCAAGAAGGATGACAAGGACAAGAAAAATAAGTACTAACC
TCCTGTACCAACTAGAGTGGCGGAAAAAGAAGAAAAAACAAAGGGACAAGATGTTGCCAGTAAACTGCCACTGGTGACAC
TTCACACTCAGTGTTGGTTAAAATTACCGAAGTTAGAGAGAATTAAAGACTATCTTCTCATGGAGGAAGAATTCATTAGA
AATCAGGAACAAATAAAACTATTAGAAGAAAAGCAAGAGGAGGGAATATCAAAAGTGGATGTCTGAGGGGGACCCCGATG
TCAGTAGGAATCTTGGAAGAGATCATCGATGACAATCATGCCATTGTGTCTACATCTGTGGGCTCAGAACACTACGTCAG
CATTCTTTCATTTGTAGACAAGGATCTGCTGGAACCTGGCTGCTTGGTTCCGCTCAGACACAAGGTACATGCCGTGATAG
GGGTGCTGATGGATGACACAGGTCCCCTGGTCACAATGATGAAGGTGGAGAAGGCCCCCCAGGAGACCTATGCCAATATT
GGGGGATTGGACAACCAAATTCAGGAAATTAAGGAATCTATGGAGCTTCCTCTCACCCATCCTGAATATTATGAAGAGAT
GGGTATAAAGTCTCCTAAAGGGGTCATTCTCTGTGGTCCACCTGGCACAGGTAAAGCCTTGTTAGCCAAAGCAGTAGCAA
ACCAAACCTCAGCCACTTTCTTGAGAGTGGTTGGCTCTGAACCTATTCGGAAGTACCTAGGTGATGGGCCCAAACTCGTA
TGGGAATTGTTTCAAGTTGCTGAAGAACATGCACCATCCATCATGTTTACTGATGAAATTGAGGCCATTAGGGACAAAAA
GATATGACTCCAATTCTGGTGGTGAGAGAGAAATTCAGCAAACAACGTTGGAATTGGAACTGTTGAACCAATTGGGTGGA
TTTGATTCTAGGGAAGATGTGAAAGTTATCATGGCCACAAAGCAAATAGAAACTTTGGATCCAGCACTTATCAGACCAGG
CCGCATTGACAAGATCGAGTTCCACCTGCCTGATGAAAAGACTAAGAAGCACATCTTTCAGATTCACACAAGCAGGATGG
CACTGGCCAATGATGTAACCCTGGACGACTTGATCTTGGCTAAATATGACTTTCTCTGGTGCTGACATCAGGGCAATCTG
TACAGAAGCTGGTCTGATGGCCTTACAGAACATAGAATGAAAGTAACAAATGATGACTTCAAAAATCTAAGAAATGTTCT
TTATAGAAACAGGAAGCATCCTGAGGGCTTATCTCTA

ORF - retro_pabe_2737 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.86 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIKD
MGQSQ.GGHGP..GKKDDKDKK.KY.PPVPTRV..K..KTKG.D.ASKLPLVT.HTQC.LKL.KLERIKD
RetrocopyMGQSQGGGHGPRRGKKDDKDKKNKY*PPVPTRVAEKEEKTKGQDVASKLPLVTLHTQCWLKLPKLERIKD
ParentalYLLMEEEFIRNQEQMKPLEEKQEEERSKVDD-LRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFV
YLLMEEEFIRNQEQ.K.LEEKQEE..SKVD..LRGTPMSVG.LEEIIDDNHAIVSTSVGSEHYVSILSFV
RetrocopyYLLMEEEFIRNQEQIKLLEEKQEEGISKVDV<LRGTPMSVGILEEIIDDNHAIVSTSVGSEHYVSILSFV
ParentalDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPE
DKDLLEPGC.V.L.HKVHAVIGVLMDDT.PLVT.MKVEKAPQETYA.IGGLDNQIQEIKES.ELPLTHPE
RetrocopyDKDLLEPGCLVPLRHKVHAVIGVLMDDTGPLVTMMKVEKAPQETYANIGGLDNQIQEIKESMELPLTHPE
ParentalYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAP
YYEEMGIK.PKGVIL.GPPGTGK.LLAKAVANQTSATFLRVVGSE.I.KYLGDGPKLV.ELF.VAEEHAP
RetrocopyYYEEMGIKSPKGVILCGPPGTGKALLAKAVANQTSATFLRVVGSEPIRKYLGDGPKLVWELFQVAEEHAP
ParentalSIVFIDEIDAI-GTKRYDSNSGGEREIQRTM--LELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGR
SI.F.DEI.AI.GTKRYDSNSGGEREIQ.T...LELLNQL.GFDSR.DVKVIMAT..IETLDPALIRPGR
RetrocopySIMFTDEIEAI>GTKRYDSNSGGEREIQQTTLELELLNQLGGFDSREDVKVIMATKQIETLDPALIRPGR
ParentalIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD-LSGADIKAICTEAGLMALR-ERRMKV
ID.KIEF.LPDEKTKK.IFQIHTSRM.LA.DVTLDDLI.AK.D..SGADI.AICTEAGLMAL..E.RMKV
RetrocopyID-KIEFHLPDEKTKKHIFQIHTSRMALANDVTLDDLILAKYD>FSGADIRAICTEAGLMALQ<EHRMKV
ParentalTNEDFKKSKENVLYKKQEGTPEGLYL
TN.DFK....NVLY......PEGL.L
RetrocopyTNDDFKNLR-NVLYRNRK-HPEGLSL

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 .00 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_2737 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2737 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2737 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3323
Pan troglodytes retro_ptro_2153
Gorilla gorilla retro_ggor_1298
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,


Copyright © RetrogeneDB 2014-2017