RetrogeneDB ID:

retro_dnov_2578

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_8711:71064..71825(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA3
Ensembl ID:ENSDNOG00000004077
Aliases:None
Description:proteasome (prosome, macropain) subunit, alpha type, 3 [Source:HGNC Symbol;Acc:9532]


Retrocopy-Parental alignment summary:






>retro_dnov_2578
AGCTCTCTCGGCACTGGGTATGACCTGTCAGCCTCTACATTCCCTCCTGATGGGAGAGTTTTTCAAGTTGAATATGCTAT
GAAGGCTGTGGAAAATAGTAGTACAGCTATTGGAATCAGATGTAAAGATGGTGTTGTCTTTGGAGTAGAAAAATTAGTCC
TTTCTAAACTTTATGAAGAAGATTCCAACAAATGGTGTTTTAATGTTGATCGGCATGCAGGAATGGTGGTAGCAGGTGTG
TTGGCAGATGCTCGTTCTTTAGCAGACATAGCAAGAGAAGAGGCTTCCAACTTTAGATCTAACTTTGGCTGTAACATTCC
ACTCAAACATCTTGCAGACAGAGTGATCATGTATGTTCATGCCTGTACACTGTACAGTGCTGTTAACCTTTTGGATGCAG
TTTCACGTTAGGGTCTTACATTGTGAATGATGGTGCACAGCTCCACAGGATTGAGCCATCAGGTGTTTCATATGGTTACT
GGGGCTGTGCCCTTGGTAAAGCCAGGCAAGCTGCAAAGACAGAAATCGAAAAGCTTCAGATGAAAGAAATGACCTGCCGT
GACGTTGTTAAAGAAGTTGCAAAAATAATTTACATAGTACATGATGAAGTTAAAGATAAAGCATTTGAACTAGAGCTCAG
CTGGGTTGGTGAATTAAGTAAAGGAAGACATGAAATTGTTCCAAAAGATATAAGGGAAGAAGCAGAGAAATATGCTAAGG
AATCTTTGAAGGAAGAAGATGAATCTGATGATGATAATATG

ORF - retro_dnov_2578 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.76 %
Parental protein coverage: 99.61 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNVD
SS.GTGYDLSASTF.PDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEE.SNK..FNVD
RetrocopySSLGTGYDLSASTFPPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEDSNKWCFNVD
ParentalRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVR-PFGCSFMLGS
RH.GM.VAG.LADARSLADIAREEASNFRSNFG.NIPLKHLADRV.MYVHA.TLYSAV..PFGCSF.LGS
RetrocopyRHAGMVVAGVLADARSLADIAREEASNFRSNFGCNIPLKHLADRVIMYVHACTLYSAVN<PFGCSFTLGS
ParentalYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDVVKEVAKIIYIVHDEVKDKAF
Y.VNDGAQL..I.PSGVSYGYWGCA.GKARQAAKTEIEKLQMKEMTCRDVVKEVAKIIYIVHDEVKDKAF
RetrocopyYIVNDGAQLHRIEPSGVSYGYWGCALGKARQAAKTEIEKLQMKEMTCRDVVKEVAKIIYIVHDEVKDKAF
ParentalELELSWVGELTKGRHEIVPKDIREEAEKYAKESLKEEDESDDNNM
ELELSWVGEL.KGRHEIVPKDIREEAEKYAKESLKEEDESDD.NM
RetrocopyELELSWVGELSKGRHEIVPKDIREEAEKYAKESLKEEDESDDDNM

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 .00 RPM 46 .09 RPM
SRP012922_cerebellum 0 .00 RPM 24 .19 RPM
SRP012922_heart 0 .00 RPM 32 .72 RPM
SRP012922_kidney 0 .00 RPM 42 .71 RPM
SRP012922_liver 0 .00 RPM 30 .81 RPM
SRP012922_lung 0 .00 RPM 32 .53 RPM
SRP012922_quadricep_muscle 0 .00 RPM 33 .41 RPM
SRP012922_spleen 0 .00 RPM 43 .95 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_2578 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 21 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000152871 retrocopy
retro_cfam_1331,
Callithrix jacchus ENSCJAG000000187321 retrocopy
retro_cjac_3974,
Dasypus novemcinctus ENSDNOG00000004077 27 retrocopies
retro_dnov_1089, retro_dnov_1115, retro_dnov_1156, retro_dnov_1240, retro_dnov_1252, retro_dnov_1285, retro_dnov_1347, retro_dnov_1473, retro_dnov_1542, retro_dnov_1604, retro_dnov_1650, retro_dnov_1662, retro_dnov_1783, retro_dnov_1785, retro_dnov_1791, retro_dnov_1880, retro_dnov_1896, retro_dnov_198, retro_dnov_2030, retro_dnov_2125, retro_dnov_2128, retro_dnov_2334, retro_dnov_2507, retro_dnov_2578 , retro_dnov_447, retro_dnov_765, retro_dnov_992,
Dipodomys ordii ENSDORG000000021671 retrocopy
retro_dord_402,
Homo sapiens ENSG000001005671 retrocopy
retro_hsap_1348,
Gorilla gorilla ENSGGOG000000158141 retrocopy
retro_ggor_1049,
Macaca mulatta ENSMMUG000000035092 retrocopies
retro_mmul_2187, retro_mmul_564,
Monodelphis domestica ENSMODG000000078391 retrocopy
retro_mdom_544,
Mustela putorius furoENSMPUG000000061262 retrocopies
retro_mputfur_1549, retro_mputfur_414,
Mus musculus ENSMUSG000000600733 retrocopies
retro_mmus_1277, retro_mmus_1463, retro_mmus_2810,
Nomascus leucogenys ENSNLEG000000130921 retrocopy
retro_nleu_1831,
Oryctolagus cuniculus ENSOCUG000000103161 retrocopy
retro_ocun_667,
Otolemur garnettii ENSOGAG000000003822 retrocopies
retro_ogar_1764, retro_ogar_2857,
Ochotona princeps ENSOPRG000000028352 retrocopies
retro_opri_67, retro_opri_991,
Pongo abelii ENSPPYG000000058552 retrocopies
retro_pabe_1120, retro_pabe_339,
Pan troglodytes ENSPTRG000000063901 retrocopy
retro_ptro_923,
Rattus norvegicus ENSRNOG000000078511 retrocopy
retro_rnor_183,
Sorex araneus ENSSARG000000026702 retrocopies
retro_sara_437, retro_sara_573,
Ictidomys tridecemlineatus ENSSTOG000000135391 retrocopy
retro_itri_1317,
Tupaia belangeri ENSTBEG000000169101 retrocopy
retro_tbel_1947,
Tursiops truncatus ENSTTRG000000135261 retrocopy
retro_ttru_545,


Copyright © RetrogeneDB 2014-2017