RetrogeneDB ID:

retro_pabe_2099

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2b:6850033..6851068(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:WBP11
Ensembl ID:ENSPPYG00000004323
Aliases:None
Description:WW domain binding protein 11 [Source:HGNC Symbol;Acc:16461]


Retrocopy-Parental alignment summary:






>retro_pabe_2099
TTAGAAATGAAGGATCCCAAACAGATTACCAGGGACATGGAGAAACTGGATGAAATGGAGTTTAACCCACTGTAACAGCC
ACAGTTAAATGAGAAAGTACTGAAAAACAAGCGTAAAAAACTGTGTGAAACCTTTGAACATATTCTATGACTCTGTCAAA
AAGAAAATCCAGACAGTTACAAGGACTTGAGAAAACTAGAAACAGAGTATGAACAGAAGAGGGCTCAACTTAGCCAATAT
TTTGATGGCTGTCGAGAATGCTCAGCATGCGGAAGTGGAGAGCATTCCTTTGCCAGATGTGCCACATGCTCCTTCCAACA
TTTTGATCCAGGACATTCCACTTCCTGGTCCCAGCCACTCTCCATCCTTAGGAAAACCTCAGCCTATGGACCTCCAACTC
GGGCAGTTTCTATCCTTCCTCTTCTTGGGCATAATGTTCCACGTTTGCCCCCCGGCAGAAAAATCTCCTGGCCCTCCCCC
AGCCCACCTCCTCCTCAAGTCTTGCACATGTATGGCCGTAAAGTGGGTTTTGCCCTAGATCTTCCCCCTCATAGGCGAGA
TGAAGAAGACACGTTATATAATCCTGAACTTGCCCGGCAAGTTCATGGTGATGATGTTTCTAGCACCAGTGAAGATGATG
GCCCTTCTGAGGACAAGGACCAACATAAGCATGGTAACAATACTGATAATTGTGACACCAACAGATGAGACGGAGAAAGT
GGGGGGATGAATTGTGCACTGTGATGATGGTGAGTGAGCCAGCAATGAAGAAAAGAACTCAGGTCTGAGTGTACGGTTTG
CAGATATGCCTGGAAAATCAAGGAAGAAAAAGAAGAACATGAAGGAGTTAACTCCTCTTCAAGCCATAGTGCTTCCATGG
CAGGTCAAGAAGTCCCTGAGGAGGGACCAGAAGTAGAGGAATTTTCAGAGGACGATGATGAAGATGATTCTGATGACTCT
GAAGCGGATAAACAATCACAAAAACAGCATAACGAAGAGTCTCATTCTGACGGCACATCCACCGCTTCTTCACAG

ORF - retro_pabe_2099 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.91 %
Parental protein coverage: 53.82 %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLKMKDPKQIIRDMEKLDEMEFNPVQQPQLNEKVLKDKRKKLRETFERILRLYEKENPDIYKELRKLEVEY
L.MKDPKQI.RDMEKLDEMEFNP..QPQLNEKVLK.KRKKL.ETFE.IL.L..KENPD.YK.LRKLE.EY
RetrocopyLEMKDPKQITRDMEKLDEMEFNPL*QPQLNEKVLKNKRKKLCETFEHIL*LCQKENPDSYKDLRKLETEY
ParentalEQKRAQLSQYFD-AVKNAQHVEVESIPLPDMPHAPSNILIQDIPLPG-AQPPSILKKTSAYGPPTRAVSI
EQKRAQLSQYFD.AV.NAQH.EVESIPLPD.PHAPSNILIQDIPLPG..QP.SIL.KTSAYGPPTRAVSI
RetrocopyEQKRAQLSQYFD>AVENAQHAEVESIPLPDVPHAPSNILIQDIPLPG<SQPLSILRKTSAYGPPTRAVSI
ParentalLPLLGHGVPRLPPGRKPPGPPPGPPPPQVVQMYGRKVGFALDLPPRRRD-EDMLYSPELAQRGHDDDVSS
LPLLGH.VPRLPPGRK...P.P.PPPPQV..MYGRKVGFALDLPP.RRD.ED.LY.PELA...H.DDVSS
RetrocopyLPLLGHNVPRLPPGRKISWPSPSPPPPQVLHMYGRKVGFALDLPPHRRDEEDTLYNPELARQVHGDDVSS
ParentalTSEDDGYPEDMDQDKHDDSTDDSDTDKSDGESD-GDE-FVHRDDGERDNNEEKKSGLSVRFADMPGKSRK
TSEDDG..ED.DQ.KH...TD..DT...DGES..GDE..VH.DDGE...NEEK.SGLSVRFADMPGKSRK
RetrocopyTSEDDGPSEDKDQHKHGNNTDNCDTNR*DGESG<GDE<IVHCDDGE*ASNEEKNSGLSVRFADMPGKSRK
ParentalKKKNMKELTPLQAMML-RMAGQEIPEEGREVEEFSEDDDDDDSDDSEAEKQSQKQHKEESHSDGTSTASS
KKKNMKELTPLQA..L..MAGQE.PEEG.EVEEFSEDDD.DDSDDSEA.KQSQKQH.EESHSDGTSTASS
RetrocopyKKKNMKELTPLQAIVL<SMAGQEVPEEGPEVEEFSEDDDEDDSDDSEADKQSQKQHNEESHSDGTSTASS
ParentalQ
Q
RetrocopyQ

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 72 .76 RPM
SRP007412_cerebellum 0 .00 RPM 38 .18 RPM
SRP007412_heart 0 .00 RPM 29 .62 RPM
SRP007412_kidney 0 .00 RPM 36 .63 RPM
SRP007412_liver 0 .00 RPM 22 .40 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_2099 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2099 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2099 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147591 retrocopy
retro_btau_20,
Canis familiaris ENSCAFG000000129262 retrocopies
retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus ENSCJAG000000216111 retrocopy
retro_cjac_1737,
Homo sapiens ENSG000000844632 retrocopies
retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla ENSGGOG000000044483 retrocopies
retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii ENSMEUG000000139711 retrocopy
retro_meug_1952,
Myotis lucifugus ENSMLUG000000152161 retrocopy
retro_mluc_1074,
Macaca mulatta ENSMMUG000000192991 retrocopy
retro_mmul_1329,
Monodelphis domestica ENSMODG000000179491 retrocopy
retro_mdom_143,
Mustela putorius furoENSMPUG000000116191 retrocopy
retro_mputfur_280,
Mus musculus ENSMUSG000000302161 retrocopy
retro_mmus_2740,
Nomascus leucogenys ENSNLEG000000039261 retrocopy
retro_nleu_2651,
Oryctolagus cuniculus ENSOCUG000000171771 retrocopy
retro_ocun_974,
Otolemur garnettii ENSOGAG000000105181 retrocopy
retro_ogar_207,
Ochotona princeps ENSOPRG000000150083 retrocopies
retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii ENSPPYG00000004323 3 retrocopies
retro_pabe_1558, retro_pabe_2099 , retro_pabe_3663,
Pan troglodytes ENSPTRG000000047243 retrocopies
retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus ENSRNOG000000055053 retrocopies
retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus ENSRNOG000000495931 retrocopy
retro_rnor_740,
Sorex araneus ENSSARG000000070851 retrocopy
retro_sara_753,
Sarcophilus harrisii ENSSHAG000000166491 retrocopy
retro_shar_81,
Tupaia belangeri ENSTBEG000000033941 retrocopy
retro_tbel_2213,


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