RetrogeneDB ID:

retro_dnov_14

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_22329:32802..34392(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000018309
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:UBQLN1
Ensembl ID:ENSDNOG00000012687
Aliases:None
Description:ubiquilin 1 [Source:HGNC Symbol;Acc:12508]


Retrocopy-Parental alignment summary:






>retro_dnov_14
ATGGCGGAAAACGGCGAGAACAGCGGCCCTCCGCGCCCCTCCCGCGGCCCAGCAGCGACCCAAGGCCCGACTGCTGCCCC
GCCTGAGCCAAAAATCATAAAAGTCACTGTGAAAACTCCCAAAGAGAAAGAGGAGTTCGCAGTGCCCGAGAATAGCTCGG
TCCAGCAGTTTAAAGAAGCGATTTCGAAACGCTTCAAGTCCCAAACCGATCAGCTAGTGCTGATTTTTGCCGGAAAAATA
TTAAAAGATCAAGATACCTTGATCCAGCACGGCATCCATGATGGACTAACTGTTCACCTTGTCATCAAAAGCCAGAACCG
ACCTCAGGGCCAGTCCACGCAGCCTAGCAATGCCGCGGGAACTAATATTACCACAGCGTCGACTCCCAGGAGTAATTCCA
CACCGATTTCTACAAATAGCAACCCGTTTGGATTGGGGAACCTGGGAGGGCTTGCAGGCCTTAGCAGCCTGGGTTTGAGC
TCAACCAGCTTTTCTGAGCTCCAGAGCCAGATGCAGCAGCAACTCATGTCCAGTCCTGAGATGATGATCCAAATAATGGA
AAATCCCTTTGTTCAGAGCATGCTTTCCAATCCCGATCTGATGAGGCAGCTCATTATGGCCAATCCACAGATGCAACAGT
TGATTCAAAGAAATCCAGAAATCAGTCACCTGCTCAACAACCCTGATATAATGAGGCAGACTCTCGAAATCGCCAGAAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAAGACCTGGCTCTGAGCAATCTTGAAAGCATCCCAGGTGGCTACAATGC
TCTACGGCGCATGTACACTGACATTCAAGAACCGATGCTGAATGCTGCACAAGAGCAATTTGGAGGTAATCCCTTTGCCT
CAGTGGGGAGCAGTTCTTCTGGGGAAGGTACACAGCCTTCCCGCACAGAAAATCGAGATCCACTGCCCAATCCATGGGCA
CCACCACCGACTACCCAGAGTTCTGCGACCACCAGCACAACCACCAGCAGCAGTGGCAGTGGGTCTGGTAGTAGCTCCAG
CAATGCTGCTGGGAACACCGTAGCTGCAGCCAATTATGTTGCTAGTGTCTTCAGTACCCCAGGAATGCAGAATCTGCTGC
AACAGATAACTGAAAACCCCCAGCTGATCCAGAATATGCTGTCTGCACCCTACATGAGAAGCATGATGCAGTCTCTGAGC
CAGAATCCAGATCTGGCTGCACAGATGATGCTGAACAACCCACTGTTTACAGGAAATCCTCAGCTGCAGGAGCAGATGCG
TCCTCAGCTCCCGGCTTTCCTGCAGCAAATGCAGAATCCAGACACACTATCAGCCATGTCTAACCCCAGAGCAATGCAGG
CTTTAATGCAGATCCAGCAGGGGCTACAGACATTAGCTACCGAAGCACCTGGCCTCATTCCAAGCTTCACTCCAGGTGTG
GGGGTGGGGGTGCTGGGAACCGCCATTGGCCCTGTAGGCCCAGTTACTCCCATAGGTCCCATAGGTCCCATTGTCCCATT
TACCCCCATAGGACCAATTGGGCCCATAGGACCCACTGGCCCTGCAGGTCCTCCTGGCCCTGCCGGCTCT

ORF - retro_dnov_14 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.05 %
Parental protein coverage: 72.12 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalPQDHSAQQTNSTGGNVTTSSAPNSNSTSGSTTSNPFGLGGLGGLAGLSSLGLNTSNFSELQSQMQRQLMS
PQ..S.Q..N..G.N.TT.S.P.SNST..ST.SNPFGLG.LGGLAGLSSLGL....FSELQSQMQ.QLMS
RetrocopyPQGQSTQPSNAAGTNITTASTPRSNSTPISTNSNPFGLGNLGGLAGLSSLGLSSTSFSELQSQMQQQLMS
ParentalNPEMMVQIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEM
.PEMM.QIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEM
RetrocopySPEMMIQIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEM
ParentalMRNQDRALSNLESIPGGYNALRRMYTDIQEPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLP
MRNQD.ALSNLESIPGGYNALRRMYTDIQEPML.AAQEQFGGNPFAS.V...SSGEG.QPSRTENRDPLP
RetrocopyMRNQDLALSNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFAS-VGSSSSGEGTQPSRTENRDPLP
ParentalNPWAPPASQSSSASSGTTNTVGGTG-GSAASGSAGQSTTAPNLGSGVGASMFNTPGMQSLLQQITENPQL
NPWAPP....SSA...TT....G.G.GS..S..AG....A.N....V....F.TPGMQ.LLQQITENPQL
RetrocopyNPWAPPPTTQSSATTSTTTSSSGSGSGSSSSNAAGNTVAAANYVASV----FSTPGMQNLLQQITENPQL
ParentalMQNMLSAPYMRSMMQSLSQNPDLAAQMMLNNPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAM
.QNMLSAPYMRSMMQSLSQNPDLAAQMMLNNPLF.GNPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAM
RetrocopyIQNMLSAPYMRSMMQSLSQNPDLAAQMMLNNPLFTGNPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAM
ParentalQALLQIQQGLQTLATEAPGLIPGFTP--GLGALGNTGGPSG
QAL.QIQQGLQTLATEAPGLIP.FTP..G.G.LG...GP.G
RetrocopyQALMQIQQGLQTLATEAPGLIPSFTPGVGVGVLGTAIGPVG

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
SRP012922_ascending_colon 23 .73 RPM 71 .18 RPM
SRP012922_cerebellum 103 .79 RPM 61 .04 RPM
SRP012922_heart 11 .37 RPM 23 .44 RPM
SRP012922_kidney 23 .82 RPM 36 .41 RPM
SRP012922_liver 12 .85 RPM 41 .18 RPM
SRP012922_lung 28 .41 RPM 41 .54 RPM
SRP012922_quadricep_muscle 25 .62 RPM 33 .23 RPM
SRP012922_spleen 31 .13 RPM 35 .37 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_14 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
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 ENSDNOG00000012687 1 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 ENSPPYG000000193231 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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