RetrogeneDB ID:

retro_mdom_1057

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:432612944..432613553(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000018083
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1057
GTTGTGCTTCCTACAAAGACTAAGTCCAATACAACACCTCAGAAATCTCAGAATGATGAAGTTCCTCTTATGCCCACCCC
ATTGCCTCCTCTGCATACGGTCTCCCGAAATAATCTGCAGACCTGGTGCCAGAGACTCAATATAAGCAAAAATGGCTGGA
AGCACATTCTATACAAGAGACTTATGGACCACATGTCACCGTCTGAGCAAGATATCCCCAATGTCGAAGAAAAGGACCAG
TGGATAAAAGTCAAGACAGAAGCTTTGCTTGAAGAGGACTCTCCAGGCGAAAGTCAGGTGATGGTTAGAGCCACAGAGCT
GTTCACCAATAATAATAATAAGAGAGAGGCCACAAAGACTTCTCTGGTCCAGATGGCCAGCATGGCAGCATGGGGCAGGC
TCATGGCCAAGGCCAAGGCCAAGGCTGTGTGGCTTGCATCTGTATCTTCTGAGCCTGCTCGGGCTGGCCAATCAGATTCC
CCACGATGGTGTGTAGTGCATGGTGAATCTTTTCCCAATGATGTCTCTGGTTTGGTTCCTCTGGAGTTCCATGCTGGACA
GACCTGGGTGCCTGATCTCTCTCCTGTTACTGCCTGCCTGTTCTTTCCC

ORF - retro_mdom_1057 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.24 %
Parental protein coverage: 90.62 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVVLPTKTKSNTTPQKSQNDEVPPMPTPLPPLHTVSRNNLQTWCQRLNISKNGRKHILYKRLMDHVSPSEQ
VVLPTKTKSNTTPQKSQNDEVP.MPTPLPPLHTVSRNNLQTWCQRLNISKNG.KHILYKRLMDH.SPSEQ
RetrocopyVVLPTKTKSNTTPQKSQNDEVPLMPTPLPPLHTVSRNNLQTWCQRLNISKNGWKHILYKRLMDHMSPSEQ
ParentalDIPTVEEKDQWIKVKTEALLEEDSPGESQAMVRAAEPFTNKKKKREATKTSLVQTASMAAWGRLMATAKA
DIP.VEEKDQWIKVKTEALLEEDSPGESQ.MVRA.E.FTN...KREATKTSLVQ.ASMAAWGRL......
RetrocopyDIPNVEEKDQWIKVKTEALLEEDSPGESQVMVRATELFTNNNNKREATKTSLVQMASMAAWGRLXXXXXX
ParentalKAVWPASVSSEPARAGQSNSPRWCVVHGESFPNDVSGSVPLEFHAGQTWVPEEDMLIPLLLLP
..VW.ASVSSEPARAGQS.SPRWCVVHGESFPNDVSG.VPLEFHAGQTWVP........L..P
RetrocopyXXVWLASVSSEPARAGQSDSPRWCVVHGESFPNDVSGLVPLEFHAGQTWVPDLSPVTACLFFP

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 0 .00 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_1057 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1057 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica 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 37 parental genes, and 96 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000204602 retrocopies
retro_btau_435, retro_btau_529,
Canis familiaris ENSCAFG000000103355 retrocopies
retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus ENSCJAG000000201684 retrocopies
retro_cjac_1378, retro_cjac_1991, retro_cjac_3832, retro_cjac_944,
Callithrix jacchus ENSCJAG000000201712 retrocopies
retro_cjac_1334, retro_cjac_1491,
Dasypus novemcinctus ENSDNOG000000107456 retrocopies
retro_dnov_1248, retro_dnov_1626, retro_dnov_1714, retro_dnov_2462, retro_dnov_2583, retro_dnov_2656,
Erinaceus europaeus ENSEEUG000000089444 retrocopies
retro_eeur_205, retro_eeur_415, retro_eeur_426, retro_eeur_616,
Echinops telfairi ENSETEG000000027221 retrocopy
retro_etel_312,
Echinops telfairi ENSETEG000000079854 retrocopies
retro_etel_2051, retro_etel_2058, retro_etel_506, retro_etel_918,
Homo sapiens ENSG000001215701 retrocopy
retro_hsap_893,
Homo sapiens ENSG000001635303 retrocopies
retro_hsap_1642, retro_hsap_2903, retro_hsap_357,
Gorilla gorilla ENSGGOG000000151212 retrocopies
retro_ggor_1970, retro_ggor_723,
Loxodonta africana ENSLAFG000000168041 retrocopy
retro_lafr_456,
Microcebus murinus ENSMICG000000137446 retrocopies
retro_mmur_1171, retro_mmur_156, retro_mmur_1634, retro_mmur_213, retro_mmur_598, retro_mmur_955,
Myotis lucifugus ENSMLUG000000074441 retrocopy
retro_mluc_1706,
Myotis lucifugus ENSMLUG000000164231 retrocopy
retro_mluc_973,
Macaca mulatta ENSMMUG000000169011 retrocopy
retro_mmul_1515,
Macaca mulatta ENSMMUG000000221123 retrocopies
retro_mmul_1550, retro_mmul_342, retro_mmul_475,
Monodelphis domestica ENSMODG00000018083 3 retrocopies
retro_mdom_1057 , retro_mdom_1478, retro_mdom_999,
Mustela putorius furoENSMPUG000000102061 retrocopy
retro_mputfur_800,
Mus musculus ENSMUSG000000585503 retrocopies
retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Mus musculus ENSMUSG000000724197 retrocopies
retro_mmus_1303, retro_mmus_1832, retro_mmus_1847, retro_mmus_2391, retro_mmus_2935, retro_mmus_3699, retro_mmus_394,
Nomascus leucogenys ENSNLEG000000040202 retrocopies
retro_nleu_1329, retro_nleu_633,
Nomascus leucogenys ENSNLEG000000040303 retrocopies
retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus ENSOCUG000000031751 retrocopy
retro_ocun_61,
Oryctolagus cuniculus ENSOCUG000000164351 retrocopy
retro_ocun_114,
Otolemur garnettii ENSOGAG000000312287 retrocopies
retro_ogar_1678, retro_ogar_1722, retro_ogar_1953, retro_ogar_2404, retro_ogar_2567, retro_ogar_2900, retro_ogar_586,
Ochotona princeps ENSOPRG000000050591 retrocopy
retro_opri_433,
Pongo abelii ENSPPYG000000135653 retrocopies
retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
Pongo abelii ENSPPYG000000135663 retrocopies
retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes ENSPTRG000000151993 retrocopies
retro_ptro_1113, retro_ptro_1962, retro_ptro_281,
Pan troglodytes ENSPTRG000000152002 retrocopies
retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus ENSPVAG000000106771 retrocopy
retro_pvam_1237,
Rattus norvegicus ENSRNOG000000254044 retrocopies
retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii ENSSHAG000000173981 retrocopy
retro_shar_542,
Tupaia belangeri ENSTBEG000000062121 retrocopy
retro_tbel_3864,
Tursiops truncatus ENSTTRG000000095001 retrocopy
retro_ttru_1524,
Tursiops truncatus ENSTTRG000000095081 retrocopy
retro_ttru_1772,


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