RetrogeneDB ID:

retro_mdom_814

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:70485777..70486419(-)
Located in intron of:ENSMODG00000005732
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000015601
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_814
ATGGCTGCCCAAGGAGAACCCCAAGTGCAGTTCAAACTTGTATTAGTTGGTGATGGAGGTACAGAAAAAACTACATTTGT
AAAATGTCACTTGACTGGTGAATTTGAGAAGAAGTATGTAGCCACCTTGGGTGTTGAGGTCCATCCCCTTGTGTTCCATA
CTAACAGAGGTCCTATTAAATTCAACATATGGGATACAGCTGGCCAAGAGTAATTTAGTGGTCTGAGAGATTACATCCAA
GCTCAGTGTGCCATTATAATGTTTGATGTAACATCAAGAGTTACTTACAAGAATGTACCTAACTGGCATAGAGATCTGGT
ACGAGTATGTGAAAATATGCCTATAGTGTTGTGTGGCAACAAAATGGATATTAAGGACAGAAAAGTCAAGGCAAAATCAA
TTGTCTTCCATAGGAAGAAGAATCTCCAGTACTATGACATTTCAGCCAAAAGTAATTACAACTTTGAGAAGCCCTTCCTT
TGGCTTGCTAGAAAACTTATTGGAGACCCTAATTTGGAGTTTGTTGCCATGCCTGCTCTTGCACCTCCAGAGGTTGTCAT
GGACCCAGCACTGGCAGCACAGTATGAGCAGGACTTACAGATTGCTCAGACAACTGTGCTCCCTGATGAAGATGATAATC
TG

ORF - retro_mdom_814 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.91 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQE
MAAQGEPQVQFKLVLVGDGGT.KTTFVK.HLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFN.WDTAGQE
RetrocopyMAAQGEPQVQFKLVLVGDGGTEKTTFVKCHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNIWDTAGQE
ParentalKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHR
.F.GLRD..YIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCEN.PIVLCGNK.DIKDRKVKAKSIVFHR
Retrocopy*FSGLRD--YIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENMPIVLCGNKMDIKDRKVKAKSIVFHR
ParentalKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEQDLQIAQTTALP
KKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEQDLQIAQTT.LP
RetrocopyKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEQDLQIAQTTVLP
ParentalDEDDDL
DEDD.L
RetrocopyDEDDNL

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_814 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_814 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 29 parental genes, and 152 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000042224 retrocopies
retro_amel_1119, retro_amel_1625, retro_amel_1631, retro_amel_700,
Canis familiaris ENSCAFG000000066706 retrocopies
retro_cfam_1406, retro_cfam_1584, retro_cfam_1604, retro_cfam_2058, retro_cfam_426, retro_cfam_899,
Callithrix jacchus ENSCJAG000000039278 retrocopies
retro_cjac_1558, retro_cjac_1844, retro_cjac_2509, retro_cjac_2952, retro_cjac_3071, retro_cjac_3107, retro_cjac_4222, retro_cjac_492,
Dasypus novemcinctus ENSDNOG0000000923012 retrocopies
retro_dnov_1154, retro_dnov_1269, retro_dnov_1485, retro_dnov_1543, retro_dnov_1585, retro_dnov_1795, retro_dnov_1924, retro_dnov_1945, retro_dnov_2142, retro_dnov_2189, retro_dnov_2613, retro_dnov_991,
Equus caballus ENSECAG000000205323 retrocopies
retro_ecab_195, retro_ecab_591, retro_ecab_680,
Echinops telfairi ENSETEG0000001187518 retrocopies
retro_etel_1051, retro_etel_1161, retro_etel_1351, retro_etel_1365, retro_etel_1584, retro_etel_1673, retro_etel_1878, retro_etel_1896, retro_etel_1915, retro_etel_2141, retro_etel_2150, retro_etel_2189, retro_etel_294, retro_etel_383, retro_etel_409, retro_etel_412, retro_etel_514, retro_etel_813,
Felis catus ENSFCAG000000273756 retrocopies
retro_fcat_1097, retro_fcat_1230, retro_fcat_1297, retro_fcat_1586, retro_fcat_1904, retro_fcat_269,
Homo sapiens ENSG000001323413 retrocopies
retro_hsap_3126, retro_hsap_3446, retro_hsap_4908,
Gorilla gorilla ENSGGOG000000153404 retrocopies
retro_ggor_2142, retro_ggor_2328, retro_ggor_2556, retro_ggor_3066,
Loxodonta africana ENSLAFG000000176731 retrocopy
retro_lafr_1253,
Microcebus murinus ENSMICG000000006534 retrocopies
retro_mmur_1270, retro_mmur_669, retro_mmur_791, retro_mmur_866,
Macaca mulatta ENSMMUG000000209272 retrocopies
retro_mmul_1990, retro_mmul_2641,
Monodelphis domestica ENSMODG00000015601 8 retrocopies
retro_mdom_100, retro_mdom_1718, retro_mdom_1990, retro_mdom_543, retro_mdom_580, retro_mdom_806, retro_mdom_814 , retro_mdom_969,
Mustela putorius furoENSMPUG000000040446 retrocopies
retro_mputfur_1190, retro_mputfur_1523, retro_mputfur_228, retro_mputfur_755, retro_mputfur_784, retro_mputfur_899,
Mus musculus ENSMUSG000000294304 retrocopies
retro_mmus_1653, retro_mmus_182, retro_mmus_2029, retro_mmus_265,
Nomascus leucogenys ENSNLEG000000082824 retrocopies
retro_nleu_1565, retro_nleu_2303, retro_nleu_2353, retro_nleu_775,
Ornithorhynchus anatinus ENSOANG000000064471 retrocopy
retro_oana_62,
Oryctolagus cuniculus ENSOCUG000000265062 retrocopies
retro_ocun_1139, retro_ocun_958,
Otolemur garnettii ENSOGAG000000250468 retrocopies
retro_ogar_1482, retro_ogar_1611, retro_ogar_2058, retro_ogar_2560, retro_ogar_2692, retro_ogar_2810, retro_ogar_377, retro_ogar_497,
Ochotona princeps ENSOPRG000000026297 retrocopies
retro_opri_1062, retro_opri_1227, retro_opri_514, retro_opri_622, retro_opri_647, retro_opri_74, retro_opri_97,
Pongo abelii ENSPPYG000000051243 retrocopies
retro_pabe_2582, retro_pabe_2853, retro_pabe_3815,
Pan troglodytes ENSPTRG000000056364 retrocopies
retro_ptro_1762, retro_ptro_2115, retro_ptro_2338, retro_ptro_3273,
Pteropus vampyrus ENSPVAG0000001474215 retrocopies
retro_pvam_1023, retro_pvam_1049, retro_pvam_1328, retro_pvam_365, retro_pvam_485, retro_pvam_597, retro_pvam_61, retro_pvam_746, retro_pvam_770, retro_pvam_863, retro_pvam_933, retro_pvam_934, retro_pvam_935, retro_pvam_948, retro_pvam_968,
Rattus norvegicus ENSRNOG000000009383 retrocopies
retro_rnor_138, retro_rnor_410, retro_rnor_917,
Sarcophilus harrisii ENSSHAG000000180181 retrocopy
retro_shar_538,
Sus scrofa ENSSSCG000000097463 retrocopies
retro_sscr_1136, retro_sscr_194, retro_sscr_771,
Ictidomys tridecemlineatus ENSSTOG000000039923 retrocopies
retro_itri_1009, retro_itri_1442, retro_itri_723,
Tursiops truncatus ENSTTRG000000127326 retrocopies
retro_ttru_1481, retro_ttru_204, retro_ttru_387, retro_ttru_439, retro_ttru_792, retro_ttru_892,
Vicugna pacos ENSVPAG000000088803 retrocopies
retro_vpac_436, retro_vpac_589, retro_vpac_85,


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