RetrogeneDB ID:

retro_pabe_87

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:57223317..57225192(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000020401
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:UBQLN1
Ensembl ID:ENSPPYG00000019323
Aliases:None
Description:ubiquilin-1 [Source:RefSeq peptide;Acc:NP_001127579]


Retrocopy-Parental alignment summary:






>retro_pabe_87
ATGGCTGAGAATGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGCGGCCCTGCCGCGGCCCAAGGCTCGGCTGCTGCCCC
GGCTGAGCCTAAAATCATCAAAGTCACTGTGAAGACTCCCAAAGAGAAAGAGGAGTTCGCGGTGCCCGAGAACAGCTCGG
TTCAGCAGTTTAAGGAAGCGATTTCGAAACGCTTCAAATCCCAAACCGATCAGCTAGTGCTGATTTTTGCCGGAAAAATC
TTAAAAGATCAAGATACCTTGATCCAGCATGGCATCCATGATGGGCTGACTGTTCACCTTGTCATCAAAAGCCAGAACCG
ACCTCAGGGCCAGTCCACGCAGCCTAGCAATGCCGCGGGAACTAACACTACCTCGGCGTCGACTCCCAGGAGTAACTCCA
CACCTATTTCCACAAATAGCAACCCGTTTGGGTTGGGGAGCCTGGGAGGACTTGCAGGCCTTAGCAGCCTGGGCTTGAGC
TCGACCAACTTCTCTGAGCTCCAGAGCCAGATGCAGCAGCAGCTTATGGCCAGCCCTGAGATGATGATCCAAATAATGGA
AAATCCCTTTGTTCAGAGCATGCTTTCGAATCCCGATCTGATGAGGCAGCTCATTATGGCTAATCCACAGATGCAGCAAT
TGATTCAGAGAAACCCAGAAATCAGTCACCTGCTCAACAACCCAGATATAATGAGGCAGACACTCGAAATTGCCAGGAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAAGACCTGGCTCTTAGCAATCTAGAAAGCATCCCAGGTGGCTATAATGC
TTTACGGCGCATGTACACTGACATTCAAGAGCCGATGCTGAATGCCGCACAAGAGCAGTTTGGGGGTAATCCATTTGCCT
CCGTGGGGAGTAGTTCCTCCTCTGGGGAAGGTACGCAGCCTTCCCGCACAGAAAATCGCGATCCACTACCCAATCCGTGG
GCACCACCGCCAGCTACCCAGAGTTCTGCAACTACCAGCACGACCACAAGCACTGGTAGTGGGTCTGGCAATAGTTCCAG
CAGTGCTACTGGGAACACCGTTGCTGCCGCTAATTATGTCGCCAGCATCTTTAGTACCCCAGGCATGCAGAGCCTGCTGC
AACAGATAACTGAAAACCCCCAGCTGATTCAGAATATGCTGTCGGCACCCTACATGAGAAGCATGATGCAGTCGCTGAGC
CAGAATCCAGATTTGGCTGCACAGATGATGCTGAATAGCCCGCTGTTTACTGCAAATCCTCAGCTGCAGGAGCAGATGCG
GCCACAGCTCCCAGCCTTCCTGCAGCAGATGCAGAATCCAGACACACTGTCAGCCATGTCAAACCCAAGAGCAATGCAGG
CTTTGATGCAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGGCCTGATTCCAAGCTTCACTCCAGGTGTG
GGGGTGGGGGTGCTGGGAACCGCTATAGGCCCTGTAGGCCCAGTCACCCCCATAGGCCCCATAGGCCCTATAGTCCCTTT
TACCCCCATAGGCCCCATTGGGCCCATAGGACCCACTGGCCCTGCAGGCCCCCCTGGCTCCACCGGCTCTGGTGGCCCCA
CTGGGCCTACTGCGTCCAGCGCTGCACCCAGTGAAACCACGAGTCCTACATCAGAATCTGGACCCAACCAGCAGTTCATT
CAGCAAATGGTGCAGGCCCTGGCTGGAGCAAGTGCTCCACAGCTGCCGAATCCAGAAGTCAGATTTCAGCAACAACTGGA
ACAGCTCAACGCAATGGGGTTCTTAAACCGTGAAGCAAACTTGCAGGCCCTAATAGCAACAGGAGGCGACATCAATGCAG
CCATTGAAAGGCTGCTGGGCTCCCAGCCATCGTAA

ORF - retro_pabe_87 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.31 %
Parental protein coverage: 61.35 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAESGESGGPPGSQDSAAGAEGAGAPAAAASAEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
MAE.GES.GPP......A.A.G.....AAA.AEPKI.KVTVKTPKEKEEFAVPENSSVQQFKE.ISKRFK
RetrocopyMAENGESSGPPRPSRGPAAAQGS----AAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFK
ParentalSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNTAGSNVTTSSTPNSNSTSG
S.TDQLVLIFAGKILKDQDTL.QHGIHDGLTVHLVIK.QNRPQ..S.Q..N.AG.N.T..STP.SNST..
RetrocopySQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAGTNTTSASTPRSNSTPI
ParentalSATSNPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQIMENPFVQSMLSNPDLMRQLIM
S..SNPFGLG.LGGLAGLSSLGL..TNFSELQSQMQ.QL...PEMM.QIMENPFVQSMLSNPDLMRQLIM
RetrocopySTNSNPFGLGSLGGLAGLSSLGLSSTNFSELQSQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLIM
ParentalANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ
ANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQ
RetrocopyANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQ
ParentalEPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWG-TASTVGGPTGSTASGTSGQSTTAP
EPML.AAQEQFGGNPFAS..S..SSGEG.QPSRTENRDPLPNPW.....T....T.ST...T...S....
RetrocopyEPMLNAAQEQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTTSTGSGSGNSS
ParentalNLVPG
....G
RetrocopySSATG

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 32 .62 RPM 126 .23 RPM
SRP007412_cerebellum 37 .57 RPM 147 .75 RPM
SRP007412_heart 8 .43 RPM 41 .27 RPM
SRP007412_kidney 11 .50 RPM 57 .64 RPM
SRP007412_liver 10 .13 RPM 55 .76 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_87 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_87 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_87 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_58
Pan troglodytes retro_ptro_93
Parental genes homology:
Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000148272 retrocopies
retro_btau_1087, retro_btau_188,
Canis familiaris ENSCAFG000000014351 retrocopy
retro_cfam_236,
Callithrix jacchus ENSCJAG000000036092 retrocopies
retro_cjac_3977, retro_cjac_4067,
Cavia porcellus ENSCPOG000000048491 retrocopy
retro_cpor_113,
Dasypus novemcinctus ENSDNOG000000126871 retrocopy
retro_dnov_14,
Dipodomys ordii ENSDORG000000152661 retrocopy
retro_dord_680,
Equus caballus ENSECAG000000191101 retrocopy
retro_ecab_1063,
Echinops telfairi ENSETEG000000028221 retrocopy
retro_etel_39,
Felis catus ENSFCAG000000150491 retrocopy
retro_fcat_83,
Homo sapiens ENSG000001350181 retrocopy
retro_hsap_58,
Myotis lucifugus ENSMLUG000000020362 retrocopies
retro_mluc_1774, retro_mluc_33,
Mustela putorius furoENSMPUG000000020281 retrocopy
retro_mputfur_55,
Mus musculus ENSMUSG000000053121 retrocopy
retro_mmus_83,
Nomascus leucogenys ENSNLEG000000033061 retrocopy
retro_nleu_31,
Otolemur garnettii ENSOGAG000000129471 retrocopy
retro_ogar_276,
Pongo abelii ENSPPYG00000019323 1 retrocopy
retro_pabe_87 ,
Pan troglodytes ENSPTRG000000210551 retrocopy
retro_ptro_93,
Rattus norvegicus ENSRNOG000000192821 retrocopy
retro_rnor_339,
Ictidomys tridecemlineatus ENSSTOG000000134621 retrocopy
retro_itri_157,
Tursiops truncatus ENSTTRG000000046961 retrocopy
retro_ttru_1475,


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