RetrogeneDB ID:

retro_mdom_1171

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:350998696..350999490(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RNPS1
Ensembl ID:ENSMODG00000015891
Aliases:None
Description:RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]


Retrocopy-Parental alignment summary:






>retro_mdom_1171
GCTCCCTCTCCCACCAAATGTAAAGATAGAACTGATGAGAAGTCAAAGGACCGGTCTAAAGATAAAGGGGCCACCAAAGA
GTAGAGTGAAAAGTACCGTGGTAGAGACAAAGCATGTAAGAAACGCAGTGCCCTCAGTGGTAGCAGTACTTCCAGGTTTC
GATCCAGTTCCACCTCTAGCTCTGGTTCTAGTACCAGCACTGGCTCTAGCAGTGGGTCTAGCTCTTCTTCCGCATCAAGC
CGTTCAGGAAGCTCTAGCACCTCCCGTAGTTCCAGCTCTAGCAGTTCCTCTGGGTCTCCAAGTCCCTCTCGACAAAGACA
TGACAATAGGAGATGGTCCCGCTCCAAATCAAAACCACCTAAAAGAGATGAAAAGGAACAAAAGAGACGAAGTCTTTACC
AAAACCCACCAAAGCACACATTGGAAGGCTCACTAAGAATGTGACAAAGGATCACATCATGGAAATATTTTCCACTTATG
GGAAAATTAAAATTATTTATATGCCTGCAGAAAGGATGCACCCTCACCTATCCAAAGGCTATGCATATGTGGAGTTTGAG
AATCCAGATGAGGCTGAAAAGGCATTGAAACACGTGGATGGAGGACAGATCGATGGTCAGGAGATAACAGCCACTGCAGT
GTTGGCTCCTTGGCCCAGGCCCCCACCCAGAAGATTTAGCCCACCTAGAAGGATGTTGCCACCTCCACCAATGTGGCGTA
GATCGCCACCACGCATGAGAAGGTCCCGCTCTCCTAGACGTAGATCTCCTATCCGCCGACGCCACCACAGCCCT

ORF - retro_mdom_1171 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.79 %
Parental protein coverage: 87.25 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAPSPTKRKDRTDEKSKDRSKDKGATKESSEKDRGRDKARKRRSASSGSSTSSRSRSSSTSSSGSSTSTGS
APSPTK.KDRTDEKSKDRSKDKGATKE.SEK.RGRDKA.K.RSA.SGSSTS.R.RSSSTSSSGSSTSTGS
RetrocopyAPSPTKCKDRTDEKSKDRSKDKGATKE*SEKYRGRDKACKKRSALSGSSTS-RFRSSSTSSSGSSTSTGS
ParentalSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRS-PSPKPTK
SSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSR.RHDNRR.SRSKSKPPKRDEKE.KRRS...PKPTK
RetrocopySSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRQRHDNRRWSRSKSKPPKRDEKEQKRRS<SLPKPTK
ParentalVHIGRLTKNVTKDHIMEIFSTYGKIKMIDMPAERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQE
.HIGRLTKNVTKDHIMEIFSTYGKIK.I.MPAERMHPHLSKGYAYVEFENPDEAEKALKH.DGGQIDGQE
RetrocopyAHIGRLTKNVTKDHIMEIFSTYGKIKIIYMPAERMHPHLSKGYAYVEFENPDEAEKALKHVDGGQIDGQE
ParentalITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSP
ITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRR.SRSPRRRSP.RRR..SP
RetrocopyITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRR-SRSPRRRSPIRRRHHSP

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_1171 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1171 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 25 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178611 retrocopy
retro_amel_194,
Bos taurus ENSBTAG000000099697 retrocopies
retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris ENSCAFG000000193971 retrocopy
retro_cfam_449,
Choloepus hoffmanni ENSCHOG000000048664 retrocopies
retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493,
Callithrix jacchus ENSCJAG000000149692 retrocopies
retro_cjac_2127, retro_cjac_3377,
Cavia porcellus ENSCPOG000000020662 retrocopies
retro_cpor_363, retro_cpor_953,
Equus caballus ENSECAG000000232881 retrocopy
retro_ecab_524,
Felis catus ENSFCAG000000076901 retrocopy
retro_fcat_248,
Homo sapiens ENSG000002059371 retrocopy
retro_hsap_2911,
Gorilla gorilla ENSGGOG000000142751 retrocopy
retro_ggor_2016,
Macropus eugenii ENSMEUG000000088821 retrocopy
retro_meug_1996,
Myotis lucifugus ENSMLUG000000168083 retrocopies
retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta ENSMMUG000000192381 retrocopy
retro_mmul_794,
Monodelphis domestica ENSMODG00000015891 1 retrocopy
retro_mdom_1171 ,
Mus musculus ENSMUSG000000346811 retrocopy
retro_mmus_173,
Oryctolagus cuniculus ENSOCUG000000043872 retrocopies
retro_ocun_1544, retro_ocun_1745,
Otolemur garnettii ENSOGAG000000315821 retrocopy
retro_ogar_3241,
Pan troglodytes ENSPTRG000000313101 retrocopy
retro_ptro_1967,
Pteropus vampyrus ENSPVAG000000051051 retrocopy
retro_pvam_296,
Rattus norvegicus ENSRNOG000000087034 retrocopies
retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii ENSSHAG000000169511 retrocopy
retro_shar_390,
Ictidomys tridecemlineatus ENSSTOG000000132001 retrocopy
retro_itri_1160,
Tupaia belangeri ENSTBEG000000090988 retrocopies
retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta ENSTSYG000000016291 retrocopy
retro_tsyr_957,
Tursiops truncatus ENSTTRG000000082207 retrocopies
retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,


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