RetrogeneDB ID:

retro_mdom_38

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:6:96440416..96441124(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000024862
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000009378
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_38
ATGTGGAGTGGACTGTTACCACCTGGGGTGAATGAAAGTGATATTGAGTTGAGTTCTGAGGATGAGACCACAGTGAAGAT
TTCAGAACTCAGTTCAAAGGAAGATAAGGGAGATGATGTAACTGGAGAAGTCAGGCTCCCTGTTTTCCATACTGGTGGAC
CTAAAAATGGGGCAGAGACAGATACAAAAAATGCTGATGAAGCGTGTCCATCTGGAGTTCCCCTAAATATGTGGAATAAG
TTTCAAGAATTACATAAAAAACATTCTGAACTGAGAACTGTAACAAATTCTAGAAGCAGAAGGACTAAAAGAAAACGTCC
CAGAAAAGATAAATTGAAGAATAATGAAGAGTCTGGCAGTCAACAATCTTTAAATGAAGCCCAGTGGAAGGAGCTTACTC
AGTATTTTGGAATAAATGATAAGTTTGAACCCCTCATAAGCAATAGAGAACTTCTAAAGTCTGGCCTTGAAGTGAGCATC
GACAAATCTGTGGCTGAAGGGGATATTGAGAAAGCAGAAGAACTAAGTAATAGGTTAGCTACTTGGGAGCTTGGAGTAAA
AATTGCCAAAGCTGTTGCTTGCCGTAATTTTGTAAAGGCTAAAAAAGATGCTGAAACTTCACAAGAGGCTCAAAAAAAGA
AGAAACTTGCATGGGGGTTTGAAGCAAAGAAGAGATGGGAAACCAAAAGCAACATGGGATATATGTAA

ORF - retro_mdom_38 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.15 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMWSGLLPPGVNESDIELSSEDETTVKISELSSKEDKGDDVTGEVRLPVFHTGGPKNGAETDTKNADEACP
MWSGLLPPGVNESDIELSSEDETTVKISELSSKEDKGDDVTGEVRLPVFHTGGPKNGAETDTKNADEACP
RetrocopyMWSGLLPPGVNESDIELSSEDETTVKISELSSKEDKGDDVTGEVRLPVFHTGGPKNGAETDTKNADEACP
ParentalSGVPLNMWNKFQELHKKHSELRTVTNSRSRRTKRKRPRKDKLKNNEESGSQQSSNEAQWKELTQYFGIND
SGVPLNMWNKFQELHKKHSELRTVTNSRSRRTKRKRPRKDKLKNNEESGSQQS.NEAQWKELTQYFGIND
RetrocopySGVPLNMWNKFQELHKKHSELRTVTNSRSRRTKRKRPRKDKLKNNEESGSQQSLNEAQWKELTQYFGIND
ParentalKFEPLISNRELLKSGLEVSIDKSVAEGDIEKAEELSNRLATRELGVKIAKAVACRNFVKAKKDAETSQEA
KFEPLISNRELLKSGLEVSIDKSVAEGDIEKAEELSNRLAT.ELGVKIAKAVACRNFVKAKKDAETSQEA
RetrocopyKFEPLISNRELLKSGLEVSIDKSVAEGDIEKAEELSNRLATWELGVKIAKAVACRNFVKAKKDAETSQEA
ParentalQKKKKLAWGFEAKKRWETKSNMGYM
QKKKKLAWGFEAKKRWETKSNMGYM
RetrocopyQKKKKLAWGFEAKKRWETKSNMGYM

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 12 .99 RPM
SRP007412_cerebellum 0 .00 RPM 3 .59 RPM
SRP007412_heart 0 .00 RPM 9 .57 RPM
SRP007412_kidney 0 .00 RPM 10 .53 RPM
SRP007412_liver 0 .00 RPM 5 .54 RPM
SRP007412_testis 0 .00 RPM 46 .36 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_38 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_38 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 47 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000001019912 retrocopies
retro_chof_1296, retro_chof_1713, retro_chof_1977, retro_chof_2137, retro_chof_2367, retro_chof_2436, retro_chof_2558, retro_chof_2685, retro_chof_590, retro_chof_639, retro_chof_698, retro_chof_832,
Callithrix jacchus ENSCJAG000000195651 retrocopy
retro_cjac_3814,
Cavia porcellus ENSCPOG000000027471 retrocopy
retro_cpor_1356,
Dasypus novemcinctus ENSDNOG000000013832 retrocopies
retro_dnov_138, retro_dnov_167,
Dipodomys ordii ENSDORG000000020741 retrocopy
retro_dord_413,
Echinops telfairi ENSETEG000000038552 retrocopies
retro_etel_1021, retro_etel_944,
Homo sapiens ENSG000001656691 retrocopy
retro_hsap_491,
Gorilla gorilla ENSGGOG000000105661 retrocopy
retro_ggor_460,
Loxodonta africana ENSLAFG000000167744 retrocopies
retro_lafr_1079, retro_lafr_332, retro_lafr_369, retro_lafr_923,
Macropus eugenii ENSMEUG000000026741 retrocopy
retro_meug_606,
Myotis lucifugus ENSMLUG000000274541 retrocopy
retro_mluc_29,
Macaca mulatta ENSMMUG000000127411 retrocopy
retro_mmul_722,
Monodelphis domestica ENSMODG00000009378 3 retrocopies
retro_mdom_112, retro_mdom_1258, retro_mdom_38 ,
Mustela putorius furoENSMPUG000000032391 retrocopy
retro_mputfur_1400,
Oryctolagus cuniculus ENSOCUG000000051501 retrocopy
retro_ocun_1487,
Otolemur garnettii ENSOGAG000000285411 retrocopy
retro_ogar_1610,
Procavia capensis ENSPCAG000000115011 retrocopy
retro_pcap_400,
Pongo abelii ENSPPYG000000026941 retrocopy
retro_pabe_242,
Pan troglodytes ENSPTRG000000029841 retrocopy
retro_ptro_370,
Pteropus vampyrus ENSPVAG000000046212 retrocopies
retro_pvam_366, retro_pvam_776,
Sorex araneus ENSSARG000000008193 retrocopies
retro_sara_258, retro_sara_323, retro_sara_541,
Sarcophilus harrisii ENSSHAG000000116013 retrocopies
retro_shar_155, retro_shar_412, retro_shar_476,
Tarsius syrichta ENSTSYG000000091471 retrocopy
retro_tsyr_518,
Tursiops truncatus ENSTTRG000000033511 retrocopy
retro_ttru_1322,


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