RetrogeneDB ID:

retro_mdom_216

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:X:29465794..29467702(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000013156
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000006222
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_216
AGTGGGGCCACCGCAATCCCAATGGCATCCCTGTATGTGGGCGATCTCCACCATGACGTGACAGAGGCAATGCTGTATGA
AAAATTCAGCCCTGCTGGGCCTATCTTGTCCATTCGAGTGTGTAGGGATATGCTCACCCGCCGTTCCCTGGGCTACGCCT
ATGTTAACTTCCAGCAGTTAGCGGATGCTGAGCGGGTGCTGGAGACCATGAACCTGGATGTGATTAAGGGCAAGCCGGTT
CGTATTATGTGGTCCCAGCGTGACCCCTCCCTGCGCAAGAGTGGCGTAGGCAACATTTTCATCAAAAATCTAGAGAAGTC
CATTGACAACAAAGCCCTGTATAAGACTTTCTCTGCCTTTGGTAATATCCTGTCCTGCAAGGTGATCAGTGATGAGAATG
GTTCTAAGGGCTATGGCTTTGTTCACTTTGAAAACCAACAGGCTGCCGACAAAGCCATTGAGAAAATGAATGGGGTACGT
CTGAATAATCTCAAAGTATATGTAGGACGCTTTAAATCCCGCAAAGAGAGAGAACTGGAACTTGGAGCTAGAGCTAGAGA
ATTCACTAATGTGTACATCAAGAATTTTGGAGAAGATATGGACAATGATAGACTTACTGAGGTCTTTGGCAAATTTGGAC
ATGCTTTGAGTGTAAAAGTGATGACTGACGAAAGTGGCAAGTCCAAAGGTTTTGGATTTGTGAGTTATGAAAAACATGAA
GATGCTCAGAGAGCTGTAGATGAAATGAATGGGAAGGAGTTCAATGGAAAGCGCATTTATGTTGGCCGAGCTCAGAAAAA
GGGAGAAAGGCAGACAGAGCTCAAGCGCCATTTTGAACAGGTGAAACAAGAGAGAAGCAGCAGATACCAAGGTGTTAACC
TGTATGTGAAAAATCTTGATGATAGCATTGATGATGAGCGTCTCCGCAAGGCGTTTTCTCCATTTGGTACAATCACCAGT
GCAAAGGTTATGATGGAAGGGGGCCACAGCAGAGGCTTCGGGTTTGTTTGTTTCTCTGCACCAGAAGAAGCTGCCAAAGC
AGTTTCCGAAATGAATGGCAAATTGGTAGCTACTAAACCTCTCTATGTAGCTTTAGCTCAGCGCAAACGAGACCGCCAGG
TTCACCTGACAAACCAATACATGCAGAGAATGGCCAGTTTCCAAGCCATGTCTAATCCAGTGTTCAGCCCCTATCAGCCA
CCTCCGACTTCCAGATACTTCATGACACCTCTTCCACAACCTCAGTCACGCCCTGCCTATTATCCTTATGGGCAAATTCC
TCAATTCAGACCGAGTCCTCCTCACTGGGCAGTTCCAGGGGGAAGATTTCATCCATTCCAGACCGTCCCAGGTGTAATGC
GTCCAAGAGGACCTGCACCTGCACCTGCACCTGCACCATTTAATCCTGTGACGTCTTCATCCGTACCAGTTTCAGCACTT
ATGAATACTCAGCATATTGTTAATCCATCAAGCCAGATGTTAGGGCCACCAAATCCACCATTTATGCCTCCCATGCGCTC
AGTTCAGCAATACAAATATGCTGCTGGAGTCCGCAATCCCAAACACCTCAATATGCCACTACCGGTTACTACTCCTCAGC
CTGCTGGCCTTTTTGAATTCCAGGAGCCTCTAACTGCTTCCATGTTAGCTGCCACTCCTCCTCAGGAGCAAAAGCAGATC
TTAGGGGAACGGCTGTTCCCTCTCATTCAAGCCCTAAATCCTGCTTTGGCTGGCAAGATCACTGGCATGCTGCTAGAGAT
CGACAACTCTGAGCTTCTTCACATGCTTGAGTCTCCTGAGTCTCTCCAGGCCAAAGTTGATGAAGCTGTGGCTGTCCTGG
AAGCTCATCAGGCTAAAGAAGCTGCTGAGAAAAAAGGTGACACTGATCCAAAGATGCCACCAGATTAA

ORF - retro_mdom_216 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.05 %
Parental protein coverage: 71.77 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF
A...PMASLYVGDLH.DVTEAMLYEKFSPAGPILSIRVCRDM.TRRSLGYAYVNFQQ.ADAER.L.TMN.
RetrocopyATAIPMASLYVGDLHHDVTEAMLYEKFSPAGPILSIRVCRDMLTRRSLGYAYVNFQQLADAERVLETMNL
ParentalDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVMVCDENGSKGYGFV
DVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNL.KSIDNKALY.TFSAFGNILSCKV...DENGSKGYGFV
RetrocopyDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLEKSIDNKALYKTFSAFGNILSCKV-ISDENGSKGYGFV
ParentalH-ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGK
H.E.Q.AA..AIEKMNG..LN..KV.VGRFKSRKERE.ELGARA.EFTNVYIKNFGEDMD..RL.E.FGK
RetrocopyHFENQQAADKAIEKMNGVRLNNLKVYVGRFKSRKERELELGARAREFTNVYIKNFGEDMDNDRLTEVFGK
ParentalFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQM
FG.ALSVKVMTDESGKSKGFGFVS.E.HEDAQ.AVDEMNGKE.NGK.IYVGRAQKK.ERQTELKR.FEQ.
RetrocopyFGHALSVKVMTDESGKSKGFGFVSYEKHEDAQRAVDEMNGKEFNGKRIYVGRAQKKGERQTELKRHFEQV
ParentalKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEM
KQ.R..RYQGVNLYVKNLDD.IDDERLRK.FSPFGTITSAKVMMEGG.S.GFGFVCFS.PEEA.KAV.EM
RetrocopyKQERSSRYQGVNLYVKNLDDSIDDERLRKAFSPFGTITSAKVMMEGGHSRGFGFVCFSAPEEAAKAVSEM
ParentalNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPP--SGYFMAAIPQTQNRAAYY
NG..VATKPLYVALAQRK..RQ.HLTNQYMQRMAS..A..NPV..PYQPP..S.YFM...PQ.Q.R.AYY
RetrocopyNGKLVATKPLYVALAQRKRDRQVHLTNQYMQRMASFQAMSNPVFSPYQPPPTSRYFMTPLPQPQSRPAYY
ParentalPASQIAQLRPS-PRWTAQGARPHPFQNMPGAIRPAAPRP
P..QI.Q.RPS.P.W...G.R.HPFQ..PG..RP..P.P
RetrocopyPYGQIPQFRPSPPHWAVPGGRFHPFQTVPGVMRPRGPAP

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_216 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_216 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 24 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003481 retrocopy
retro_amel_1650,
Choloepus hoffmanni ENSCHOG000000081781 retrocopy
retro_chof_2531,
Callithrix jacchus ENSCJAG000000158335 retrocopies
retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus ENSCPOG000000129171 retrocopy
retro_cpor_1324,
Dasypus novemcinctus ENSDNOG000000087182 retrocopies
retro_dnov_1530, retro_dnov_2259,
Felis catus ENSFCAG000000018741 retrocopy
retro_fcat_1927,
Homo sapiens ENSG000000707561 retrocopy
retro_hsap_88,
Gorilla gorilla ENSGGOG000000067851 retrocopy
retro_ggor_1986,
Myotis lucifugus ENSMLUG000000122451 retrocopy
retro_mluc_579,
Macaca mulatta ENSMMUG000000177862 retrocopies
retro_mmul_1462, retro_mmul_895,
Monodelphis domestica ENSMODG00000006222 4 retrocopies
retro_mdom_123, retro_mdom_1867, retro_mdom_216 , retro_mdom_43,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mus musculus ENSMUSG000000222832 retrocopies
retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys ENSNLEG000000031423 retrocopies
retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
retro_ocun_13,
Pongo abelii ENSPPYG000000187903 retrocopies
retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus ENSPVAG000000166402 retrocopies
retro_pvam_10, retro_pvam_855,
Rattus norvegicus ENSRNOG000000086393 retrocopies
retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii ENSSHAG000000112671 retrocopy
retro_shar_24,
Sus scrofa ENSSSCG000000060632 retrocopies
retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus ENSSTOG000000163952 retrocopies
retro_itri_139, retro_itri_48,
Tarsius syrichta ENSTSYG000000042292 retrocopies
retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus ENSTTRG000000046892 retrocopies
retro_ttru_1050, retro_ttru_1812,
Vicugna pacos ENSVPAG000000038654 retrocopies
retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,


Copyright © RetrogeneDB 2014-2017