RetrogeneDB ID:

retro_dnov_1811

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_31447:43449..44666(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000008929
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSDNOG00000019151
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_dnov_1811
TTTGTGTCCTTCTTGGACAGAACTGATTGTACTCCCATTCAGTTTGAATCTGCTTGGGCACTCACTAACATTGCTTCTGG
GACATCAGAACAGACCAAGGCTGTGGTAGACGGAGGTGGTATCCCAGCATTCGTTTCTTTGTTGGCATCTCCCCATGCTC
ACATCAGTGAACAAGCTGTCTGGGCTCTAGGAAACATTGCAGGTGATGGCTCAGCTTTCCGAGACTTGGTTATCAAATAT
GGTGCAATTGATCCTCTGTTGGCTCTGCTTGCACCTCCTAACATGTCATCTTTAGCATATAGTTACTTACGTAATCTTAC
CTGGACACTTTCAAACCTTTGTCGAAACAAGAATCCTGCACCCCCTTTAGATGCTGTTGAGCAAATTCTTCCTACTCTCG
TTCGTCTCCTGCATCATGATGATCCAGAAGTATTAACAGATACCTGCTGGGCCATTTCCTATCTTACTGATGGTCCAAAT
GAACGGATTGAAATGGTTGTGAAAACTGGAGTTGTGCCTCAGCTTGTGAAGCTCCTTGGGGCTACTCAATTGCCATTGTG
ACTCCTGCACTAAGAGTCATAGGGAATATTGTTACTGGGACAGATGAACAGACTCAGGTTGTAATAGATGCAGGAGCACT
TGCTGTCTTTCCCAGCCTGCTAACTAATTCCAAAAATAATATTCAGAAGGAAGCTACCTGGACAATGTCAAACATCACAG
CTGGCTGTCAGGACCAGATACAGCAAGTAGTGAATCATGGATTGGTCCCTTTCCTTGTTAGCGTTCTTTCTCAGGCAGAG
TTTAAGACACAAAAGGAAGCTGTATGGGCTGTGACCAACTATACAAGTGGTGGAACAGTTGAACAGATTGTATACCTTTT
CCATTGTGACATAATAGAACCATTGATGAACCTTTTAACTGCAAAGGATACCAAAATTATTCTGGTTATTCTCGATGCCA
TTTCAAATATCTTTCAGGCTGCTGAGAAACTAGGTGAAACTGAGAAACTTAGTATAATGATTGAAGAATGTGGAGGCTTG
GACAAAATTGAAGCTCTACAAAACCATGAAAATGAGTCTGTTTACAAGGCTTCATTAAGCTTGATTGAGAAGTATTTCTC
TGTAGAGGAAGAAGAAGATCAGAATGTTGTGCCAGAAACTACCTCTGAAGGCTATACCTTCCAAGTTCAGGATGGTACTC
CTGGGACTTTTAACTTT

ORF - retro_dnov_1811 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.53 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalFVSFLDRTDCTPIQFESAWALTNIASGTSEQTKAVVDGGGIPAFVSLLASPHAHISEQAVWALGNIAGDG
FVSFLDRTDCTPIQFESAWALTNIASGTSEQTKAVVDGGGIPAFVSLLASPHAHISEQAVWALGNIAGDG
RetrocopyFVSFLDRTDCTPIQFESAWALTNIASGTSEQTKAVVDGGGIPAFVSLLASPHAHISEQAVWALGNIAGDG
ParentalSAFRDLVIKYGAIDPLLALLAPPNMSSLAYSYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLIRLLHHD
SAFRDLVIKYGAIDPLLALLAPPNMSSLAYSYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTL.RLLHHD
RetrocopySAFRDLVIKYGAIDPLLALLAPPNMSSLAYSYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHD
ParentalDPEVLTDTCWAISYLTDGPNERIEMVVKTGVVPQLVKLLGATQLP-IVTPALRAIGNIVTGTDEQTQVVI
DPEVLTDTCWAISYLTDGPNERIEMVVKTGVVPQLVKLLGATQLP.IVTPALR.IGNIVTGTDEQTQVVI
RetrocopyDPEVLTDTCWAISYLTDGPNERIEMVVKTGVVPQLVKLLGATQLP<IVTPALRVIGNIVTGTDEQTQVVI
ParentalDAGALAVFPSLLTNSKNNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSQAEFKTQKEAVWAVT
DAGALAVFPSLLTNSKNNIQKEATWTMSNITAG.QDQIQQVVNHGLVPFLVSVLSQAEFKTQKEAVWAVT
RetrocopyDAGALAVFPSLLTNSKNNIQKEATWTMSNITAGCQDQIQQVVNHGLVPFLVSVLSQAEFKTQKEAVWAVT
ParentalNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDK
NYTSGGTVEQIVYL.HC.IIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDK
RetrocopyNYTSGGTVEQIVYLFHCDIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDK
ParentalIEALQNHENESVYKASLSLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDGTPGTFNF
IEALQNHENESVYKASLSLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDGTPGTFNF
RetrocopyIEALQNHENESVYKASLSLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDGTPGTFNF

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 5 .83 RPM 30 .34 RPM
SRP012922_cerebellum 0 .82 RPM 8 .94 RPM
SRP012922_heart 0 .93 RPM 8 .82 RPM
SRP012922_kidney 0 .27 RPM 6 .30 RPM
SRP012922_liver 0 .31 RPM 4 .02 RPM
SRP012922_lung 1 .68 RPM 9 .77 RPM
SRP012922_quadricep_muscle 2 .08 RPM 14 .71 RPM
SRP012922_spleen 4 .81 RPM 33 .99 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_1811 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 23 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus ENSBTAG000000122251 retrocopy
retro_btau_1830,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG00000019151 6 retrocopies
retro_dnov_1184, retro_dnov_1811 , retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000205732 retrocopies
retro_ecab_1017, retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG000000049762 retrocopies
retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Tupaia belangeri ENSTBEG0000000627414 retrocopies
retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,


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