RetrogeneDB ID:

retro_mdom_234

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:X:19854034..19855711(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000014514
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000002417
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_234
AAAGCAGACGGCTTCATGGCGGCTGCCAAGAAAACCGTTTTGGGGCCCTTGATTGGCGCTATTGATCAAGGGACCAGCTC
CACTCGCTTTCTGGTGTTTAATTCTAAAACATCCGAGCTCCTGAGTCACCACCAATTCGAGCTGAAGCAGAAGTTTCCTA
AGGAAGGCTGGGTAGAGCAAGATCCGAAAGAAATCCTGCTCTCCGTCTACGAGTGTGTCGAGAAAACCTGTGAGAAGCTG
ATCCAGCTCAATGTTGACATCTCCAACATCAAAGCCATTGGGGTGAGTAACCAGAGGGAGACTACTGTCATTTGGGACAA
GTTTACCGGGGAGCCCCTCTATAATGCCGTGGTGTGGCTTGACCTCCGTACCCAGTCAACCGTTGAGACCCTCAGTAAGA
GAATCCCCGGCAATAACAATTTTGTCAAATCAAAGACCGGTCTGCCCCTGAGTACTTACTTTAGTGCTGTGAAGCTCCAT
TGGCTCCTGGAGAATGTGAGAAAAGTTAAGAAAGCTGTTGAGGAACAAAGGGCCCTTTTTGGTACCATTGACTCTTGGCT
GATCTGGAATCTGACTGGAGGTACCACGGGAGGGGTCCACTGCACAGATGTTACTAATGCAAGCAGAACCATGCTTTTCA
ACATTCATTCTCTAGAATGGGATCCAGAGTTGTGTGAGTTTTTTGATGTTCCTATGGAAATACTTCCAGATGTCCGCAGT
TCTTCCGAGATCTATGGACTGATGAAATCTGGATCTCTGGAAGGGGTACCATTATCTGGATGTTTGGGTGACCAATCTGC
AGCTTTAGTGGGACAAATGTGTTTCCAGGAAGGCCAGGCCAAAAACACCTATGGAACTGGTTGCTTCTTACTGTGCAATA
CAGGCCCCAAATGTGTATTCTCTGAACATGGCCTTCTAACCACCGTGGCTTACAAGCTGGGCAGAGACAAACCTGTATGC
TATGCCCTGGAAGGATCTGTTGCCATTGCTGGAGCAGTTGTTCGCTGGCTAAAAGACAATCTTGGCATCATAAAAACAGT
ACCAGAAATTGAAAAACTGGCCGAAGAGGCGGGCACATCTTATGGCTGCTACTTTGTTCCAGCTTTCTCAGGTTTATATG
CTCCATACTGGGAACCAAGTGCAAGAGGTATTATTTGTGGCCTTACTCAGTTCACAAATAAACAACATATTGCTTTTGCA
GCATTAGAGGCAGTATGTTTCCAAACCCGTGAAATACTAGATGCCATGAATAAAGATTGTGGAATGCCACTCACTCATCT
ACAAGCAGATGGAGGAATGACCACAAACAGAATTCTAATGCAGCTTCAAGCAGATATCCTGTATATTCCAGTAGTGAAGC
CTTCAATGCCTGAAACAACTGCCCTGGGCGCAGCCATGGCAGCTGGGTATGCTGAAGGAGTTGGAGTTTGGAGTCTTGAA
CCTGAAGATCTATCCGTTGTCACCATGGAACGCTTTGAACCCCAGATAAATGCAGAAGAAAGTGAAATTCGTTATGCCAC
TTGGAAGAAAGCTGTACAGAAATCGATGGGGTGGGTTACATCGCAAACCCCTCTACTTGGTGATTCCAATATCTTCTGTA
GTATCCCGTTGGGCTTTTATATTGTATCCAGCATGGTGATGTTAATTGGAGCAAGGTACATCTCAGGAATTCCATAA

ORF - retro_mdom_234 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.31 %
Parental protein coverage: 99.82 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAAGKANLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVELEQKFPKEGWVEQDPKEILQSVYECIERTC
AA.K..LGPL.GA.DQGTSSTRFLVFNSKT.ELLSHHQ.EL.QKFPKEGWVEQDPKEIL.SVYEC.E.TC
RetrocopyAAKKTVLGPLIGAIDQGTSSTRFLVFNSKTSELLSHHQFELKQKFPKEGWVEQDPKEILLSVYECVEKTC
ParentalDKLTELNIDISSIKAIGVSNQRETTIIWDKYTGEPLYNAVVWLDLRTQGTVETLSKRIPGNNNFVKSKTG
.KL..LN.DIS.IKAIGVSNQRETT.IWDK.TGEPLYNAVVWLDLRTQ.TVETLSKRIPGNNNFVKSKTG
RetrocopyEKLIQLNVDISNIKAIGVSNQRETTVIWDKFTGEPLYNAVVWLDLRTQSTVETLSKRIPGNNNFVKSKTG
ParentalLPLSTYFSAVKLHWILENVRKVKKAVEEERALFGTVDSWLIWSLTGGPNGGVHCTDVTNASRTMLFNIHS
LPLSTYFSAVKLHW.LENVRKVKKAVEE.RALFGT.DSWLIW.LTGG..GGVHCTDVTNASRTMLFNIHS
RetrocopyLPLSTYFSAVKLHWLLENVRKVKKAVEEQRALFGTIDSWLIWNLTGGTTGGVHCTDVTNASRTMLFNIHS
ParentalLEWDVELCEFFEVPMTILPNIRSSSEIYGLMKAGALEGVPLSGCLGDQSAALVGQMCFQDGQAKNTYGTG
LEWD.ELCEFF.VPM.ILP..RSSSEIYGLMK.G.LEGVPLSGCLGDQSAALVGQMCFQ.GQAKNTYGTG
RetrocopyLEWDPELCEFFDVPMEILPDVRSSSEIYGLMKSGSLEGVPLSGCLGDQSAALVGQMCFQEGQAKNTYGTG
ParentalCFLLCNTGQKCVFSDHGLLTTVAYKLGRDKPVCYALEGSVAIAGAVIRWLRDNLGILKTSEEIEKLAKEA
CFLLCNTG.KCVFS.HGLLTTVAYKLGRDKPVCYALEGSVAIAGAV.RWL.DNLGI.KT..EIEKLA.EA
RetrocopyCFLLCNTGPKCVFSEHGLLTTVAYKLGRDKPVCYALEGSVAIAGAVVRWLKDNLGIIKTVPEIEKLAEEA
ParentalGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTSKQHIAFAALEAVCFQTKEILDAMNKDCGIPLTHL
GTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFT.KQHIAFAALEAVCFQT.EILDAMNKDCG.PLTHL
RetrocopyGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKQHIAFAALEAVCFQTREILDAMNKDCGMPLTHL
ParentalQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQIN
Q.DGGMT.N.ILMQLQADILYIPVVKPSMPETTALGAAMAAG.AEGVGVWSLEPEDLS.VTMERFEPQIN
RetrocopyQADGGMTTNRILMQLQADILYIPVVKPSMPETTALGAAMAAGYAEGVGVWSLEPEDLSVVTMERFEPQIN
ParentalPEESEIRYAIWKKAVQKSMGWATGQTSPNAGDPNIFCSVPLGFFIVSSMVMLIGARYISGIP
.EESEIRYA.WKKAVQKSMGW.T.QT.P..GD.NIFCS.PLGF.IVSSMVMLIGARYISGIP
RetrocopyAEESEIRYATWKKAVQKSMGWVTSQT-PLLGDSNIFCSIPLGFYIVSSMVMLIGARYISGIP

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_234 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_234 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 21 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091611 retrocopy
retro_amel_45,
Canis familiaris ENSCAFG000000137131 retrocopy
retro_cfam_19,
Callithrix jacchus ENSCJAG000000076333 retrocopies
retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus ENSCPOG000000032612 retrocopies
retro_cpor_11, retro_cpor_20,
Equus caballus ENSECAG000000035991 retrocopy
retro_ecab_9,
Echinops telfairi ENSETEG000000082792 retrocopies
retro_etel_2000, retro_etel_247,
Felis catus ENSFCAG000000042641 retrocopy
retro_fcat_140,
Homo sapiens ENSG000001988144 retrocopies
retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana ENSLAFG000000076321 retrocopy
retro_lafr_30,
Myotis lucifugus ENSMLUG000000010462 retrocopies
retro_mluc_151, retro_mluc_853,
Monodelphis domestica ENSMODG00000002417 1 retrocopy
retro_mdom_234 ,
Mus musculus ENSMUSG000000250592 retrocopies
retro_mmus_119, retro_mmus_97,
Nomascus leucogenys ENSNLEG000000101022 retrocopies
retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus ENSOCUG000000130232 retrocopies
retro_ocun_2, retro_ocun_81,
Otolemur garnettii ENSOGAG000000169521 retrocopy
retro_ogar_261,
Pteropus vampyrus ENSPVAG000000124601 retrocopy
retro_pvam_1417,
Rattus norvegicus ENSRNOG000000341162 retrocopies
retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii ENSSHAG000000064701 retrocopy
retro_shar_35,
Sus scrofa ENSSSCG000000122022 retrocopies
retro_sscr_479, retro_sscr_59,
Ictidomys tridecemlineatus ENSSTOG000000087321 retrocopy
retro_itri_1436,
Tarsius syrichta ENSTSYG000000082491 retrocopy
retro_tsyr_29,


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