RetrogeneDB ID:

retro_mdom_282

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:159829608..159830715(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000024986
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DDI2
Ensembl ID:ENSMODG00000003515
Aliases:None
Description:DNA-damage inducible 1 homolog 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24578]


Retrocopy-Parental alignment summary:






>retro_mdom_282
ATGCTGCTCACTGTGTACTGCGTGCGGAGGGACTCCACTGAGATGACCTTTTCCCTCCAGGTTGACCGGGACTTTGAGCT
CCACAACTTCCGCGTGCTCTGCGAGCTGGAGTCTGGCATCCCTGCGGACGAGACGCACATTGTCTTTGCAGAGAACTCTC
TGGAAGATAACCACAGATCTTTGGCATCCTATGGCCTGAAAGATGGTGATGTAGTCATTTTAAGACAGAAAGCGAATGAA
AGGGCAGGCTCGCCAGGTCAGTTCACAGGGATAGACTTCAGCAGTATAGCAGTGCCGGGCCCATCAGGGACGTCCCGCTC
CCCGCACCAGATGCAGCCTCCCCTTTCTTCGGGAAATGTGGTGCAGGTCGCAGAAAGTCCAGCAGCACTCCGAGACATGT
TACTTTCCAACCCTCATGAATTGGCTGTGCTCAGGGAGCGCAACCCATCTCTGGCAGAAGCCCTTTTCAGTGGGGATCTT
GAGGAATTTACTAGGGTCTTGATAGAACAACAGGAAGACCAAGCGCTCAGAGATGAGGAGAGGTTTCGACTCTATGTCGC
TGATCCCTTTGATCTTGAAGCACAGGCCAAGATAGAAGAAGCCATCAGGCAACAGAACATTGAGGAAAACATGTCTATAG
CAATGGAAGAGGCCCCTGAGAGCTTTGGCCAAGTAGTGATGCTCTATATCAACTGCAAAGTGAATGGACATCCTGTGAAA
GCCTTTGTTGATACAGGTGCCCAGATGACTATTATGAGTCAAGCTTGTGCAATACGATGTAATATATTGAGACTTGTGGA
CCGAAGGTGGGCAGGGATTGCTAAAGGGGTTGGGACCCAGAAGATTATTGGTAGGGTACATCTAGCTCAGGTTCAGATTG
AAGGAGATTTTCTGGCATGTTCTTTTTCCATAATAGAAGAACAGCCCATGGATATGCTACTGGGCTTGGATATGCTCAAG
CGACATCAATGTAACATTGACCTCAAGAAAAATGTACTAGTAATTGGTACAACAGGCACACACACAGCATTCCTTCCAGA
GAGGGAACTCCCAGAATGTGCAAGATTGGCATACGATCCAGGACAAGATGATCTGCGAATGGAAGAG

ORF - retro_mdom_282 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.19 %
Parental protein coverage: 94.47 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMLLTVYCVRRDLSEVTFSLQVDADFELHNFRALCELESGIPAAESQIVYAERPLTDNHRSLASYGLKDGD
MLLTVYCVRRD..E.TFSLQVD.DFELHNFR.LCELESGIPA.E..IV.AE..L.DNHRSLASYGLKDGD
RetrocopyMLLTVYCVRRDSTEMTFSLQVDRDFELHNFRVLCELESGIPADETHIVFAENSLEDNHRSLASYGLKDGD
ParentalVVILRQKENAEPRPSVQFPSLPRIDFSSIAVPGTSGSRPHQQPAQPPRTSPADTASSPQGLDNPALLRDM
VVILRQK.N.......QF.....IDFSSIAVPG.SG........QP....P.......Q....PA.LRDM
RetrocopyVVILRQKANERAGSPGQFTG---IDFSSIAVPGPSGTSRSPHQMQP----PLSSGNVVQVAESPAALRDM
ParentalLLANPHELSLLKERNPPLAEALLSGDLEKFTKVLIEQQQDRARREQERIRLFAADPFDLEAQAKIEEDIR
LL.NPHEL..L.ERNP.LAEAL.SGDLE.FT.VLIEQQ.D.A.R..ER.RL..ADPFDLEAQAKIEE.IR
RetrocopyLLSNPHELAVLRERNPSLAEALFSGDLEEFTRVLIEQQEDQALRDEERFRLYVADPFDLEAQAKIEEAIR
ParentalQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHPVKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGI
QQNIEENM.IAMEEAPESFGQVVMLYINCKVNGHPVKAFVD.GAQMTIMSQACA.RCNI.RLVDRRWAGI
RetrocopyQQNIEENMSIAMEEAPESFGQVVMLYINCKVNGHPVKAFVDTGAQMTIMSQACAIRCNILRLVDRRWAGI
ParentalAKGVGTQKIIGRVHLAQVQIEGDFLPCSFSILEEQPMDMLLGLDMLKRHQCSIDLKKNVLVIGTTGTQTT
AKGVGTQKIIGRVHLAQVQIEGDFL.CSFSI.EEQPMDMLLGLDMLKRHQC.IDLKKNVLVIGTTGT.T.
RetrocopyAKGVGTQKIIGRVHLAQVQIEGDFLACSFSIIEEQPMDMLLGLDMLKRHQCNIDLKKNVLVIGTTGTHTA
ParentalFLPEGELPECARLAYGSGRDDIRPEE
FLPE.ELPECARLAY..G.DD.R.EE
RetrocopyFLPERELPECARLAYDPGQDDLRMEE

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_282 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_282 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 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000118731 retrocopy
retro_amel_10,
Bos taurus ENSBTAG000000187182 retrocopies
retro_btau_15, retro_btau_650,
Canis familiaris ENSCAFG000000162201 retrocopy
retro_cfam_193,
Callithrix jacchus ENSCJAG000000086251 retrocopy
retro_cjac_196,
Cavia porcellus ENSCPOG000000208851 retrocopy
retro_cpor_88,
Equus caballus ENSECAG000000007621 retrocopy
retro_ecab_110,
Homo sapiens ENSG000001973121 retrocopy
retro_hsap_96,
Gorilla gorilla ENSGGOG000000135371 retrocopy
retro_ggor_143,
Macropus eugenii ENSMEUG000000061481 retrocopy
retro_meug_1364,
Myotis lucifugus ENSMLUG000000306691 retrocopy
retro_mluc_68,
Macaca mulatta ENSMMUG000000199121 retrocopy
retro_mmul_231,
Monodelphis domestica ENSMODG00000003515 1 retrocopy
retro_mdom_282 ,
Mustela putorius furoENSMPUG000000163321 retrocopy
retro_mputfur_1509,
Mus musculus ENSMUSG000000785151 retrocopy
retro_mmus_67,
Oryctolagus cuniculus ENSOCUG000000238911 retrocopy
retro_ocun_249,
Otolemur garnettii ENSOGAG000000277091 retrocopy
retro_ogar_4,
Ochotona princeps ENSOPRG000000184481 retrocopy
retro_opri_4,
Pongo abelii ENSPPYG000000018411 retrocopy
retro_pabe_158,
Pan troglodytes ENSPTRG000000240591 retrocopy
retro_ptro_570,
Pteropus vampyrus ENSPVAG000000050841 retrocopy
retro_pvam_420,
Rattus norvegicus ENSRNOG000000122741 retrocopy
retro_rnor_2606,
Sus scrofa ENSSSCG000000034621 retrocopy
retro_sscr_6,
Ictidomys tridecemlineatus ENSSTOG000000194471 retrocopy
retro_itri_93,
Tarsius syrichta ENSTSYG000000025221 retrocopy
retro_tsyr_1120,


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