RetrogeneDB ID:

retro_dnov_2380

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_69088:3172..3901(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IGBP1
Ensembl ID:ENSDNOG00000014731
Aliases:None
Description:immunoglobulin (CD79A) binding protein 1 [Source:HGNC Symbol;Acc:5461]


Retrocopy-Parental alignment summary:






>retro_dnov_2380
AAACAAGTCAACCACAACAAGCTGCCAGATCCTTTGCATGTGGGCTGGAGAACACTTTCTGAGCTACTTAACTCAGTGTC
ATTACTATCATGTGGCTGACTTTGAGCTGCCCAAAACCAAGAACTCAGCTGATAATAACACTGCTCCTCCATGGCCTAGC
CTAGCCTTATTGCTATGGCATCTCAAAGACAGGCTAGAAGAGAGTGATACAAGCACAGGGAGGTGGAGCATAGAATATTT
ACACTGAAATCTTCTATGGAAAATGGTCAAGCAGATGATGAGTTTGTGAATATTATCTCCTTCACCTTCAGAGGTGGATT
GGTATCAGCTTGGAGGAGATTGAGAGTACTGAACAGCAAAATAAAGATCCTGAGAAAAAAAGACTCCTCAAGAGAGGCAT
CAACTTCTTGCTCATCTTGCCAGGACAGGCCTCCAATGAAGTCCTTCATTCTCACTTGGGACATGGCACAAGCCAAGGTA
TTTGGAGATGGTTATCCAAATCTGGCAACCAGCACAGTGAATGACTGGTATGATCAGCATCGGAAATATGGAGCATTACC
AGATGTGGTGATGCTCCATACAACACCAGAGTTCAAAAGAGCAGCTCAGCAGCAGGAAGACAGGGAGCAAAGAGGAGGAA
GACACTGATGGAAAATACTACCCAGAGCTTGGAAGTGGGATGACCAGAAGGATACCCACCCTAGGGGTTGTGGCAACTGA
CAGAACATG

ORF - retro_dnov_2380 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.72 %
Parental protein coverage: 72.94 %
Number of stop codons detected: 3
Number of frameshifts detected: 6


Retrocopy - Parental Gene Alignment:

ParentalKQVNPSKRLDHLQR-AREHFLNYLTQCHYYHVAEFEIPKTKNNSTENNTAS-SSMAYPSLVAMASQRQAK
KQVN..K..D.L...A.EHFL.YLTQCHYYHVA.FE.P..K......N....SSMA.PSL.AMASQRQA.
RetrocopyKQVNHNKLPDPLHV>AGEHFLSYLTQCHYYHVADFELP--KTKNSADNNTA<SSMA*PSLIAMASQRQAR
ParentalVERYKQKKELEHRLSALKSSVENGQADDER-VREYYLLHLQRWIGVSLEEIESIDQE-MKILREKDFSKE
.E.YK...E.EHR...LKSS.ENGQA.D...V.EYYLLHLQRWIG.SLEEIES..Q...KILR.KD.S.E
RetrocopyRE*YKHR-EVEHRIFTLKSSMENGQA-DDE<VCEYYLLHLQRWIGISLEEIESTEQQ>IKILRKKDSSRE
ParentalASTSRSSRQDRPPVKPFILTRDVAQAKVFGAGYPSLATMTVDDWYDQHRKYGALPDQGIAKATPAEFKKA
ASTS.SS.QDRPP.K.FILT.D.AQAKVFG.GYP.LAT.TV.DWYDQHRKYGALPD......TP.EFK.A
RetrocopyASTSCSSCQDRPPMKSFILTWDMAQAKVFGDGYPNLATSTVNDWYDQHRKYGALPDVVMLHTTP-EFKRA
ParentalAQQQEDQEQK-EEDADE-KTLHRAREWDDWKDTHPRGYGNRQNM
AQQQED.EQ..EED.D..K.L.RA..WDD.KDTHPRG.GN.QNM
RetrocopyAQQQEDREQR>EEDTDG<KILPRAWKWDDQKDTHPRGCGN*QNM

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 0 .19 RPM 19 .84 RPM
SRP012922_cerebellum 0 .27 RPM 19 .25 RPM
SRP012922_heart 0 .00 RPM 6 .73 RPM
SRP012922_kidney 0 .27 RPM 18 .34 RPM
SRP012922_liver 0 .15 RPM 11 .46 RPM
SRP012922_lung 0 .15 RPM 14 .36 RPM
SRP012922_quadricep_muscle 0 .00 RPM 19 .56 RPM
SRP012922_spleen 0 .11 RPM 13 .28 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_2380 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 19 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000077971 retrocopy
retro_btau_215,
Choloepus hoffmanni ENSCHOG000000136543 retrocopies
retro_chof_1523, retro_chof_2206, retro_chof_438,
Callithrix jacchus ENSCJAG000000125256 retrocopies
retro_cjac_111, retro_cjac_1225, retro_cjac_2278, retro_cjac_2968, retro_cjac_3417, retro_cjac_47,
Cavia porcellus ENSCPOG000000107971 retrocopy
retro_cpor_44,
Dasypus novemcinctus ENSDNOG00000014731 5 retrocopies
retro_dnov_1160, retro_dnov_2029, retro_dnov_2340, retro_dnov_2380 , retro_dnov_678,
Echinops telfairi ENSETEG000000033971 retrocopy
retro_etel_1637,
Felis catus ENSFCAG000000296881 retrocopy
retro_fcat_23,
Homo sapiens ENSG000000892895 retrocopies
retro_hsap_1317, retro_hsap_1848, retro_hsap_2766, retro_hsap_2919, retro_hsap_3059,
Gorilla gorilla ENSGGOG000000277952 retrocopies
retro_ggor_112, retro_ggor_2020,
Myotis lucifugus ENSMLUG000000041791 retrocopy
retro_mluc_316,
Macaca mulatta ENSMMUG000000139292 retrocopies
retro_mmul_1545, retro_mmul_31,
Mus musculus ENSMUSG000000312211 retrocopy
retro_mmus_169,
Nomascus leucogenys ENSNLEG000000007475 retrocopies
retro_nleu_1399, retro_nleu_1653, retro_nleu_2334, retro_nleu_671, retro_nleu_828,
Otolemur garnettii ENSOGAG000000117971 retrocopy
retro_ogar_110,
Pongo abelii ENSPPYG000000204354 retrocopies
retro_pabe_1099, retro_pabe_1451, retro_pabe_2245, retro_pabe_2533,
Pan troglodytes ENSPTRG000000219905 retrocopies
retro_ptro_1233, retro_ptro_1873, retro_ptro_1973, retro_ptro_1982, retro_ptro_901,
Pteropus vampyrus ENSPVAG000000054831 retrocopy
retro_pvam_1462,
Rattus norvegicus ENSRNOG000000262671 retrocopy
retro_rnor_311,
Tarsius syrichta ENSTSYG000000062142 retrocopies
retro_tsyr_1537, retro_tsyr_2131,


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