RetrogeneDB ID:

retro_mdom_1420

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:389707904..389709068(-)
Located in intron of:ENSMODG00000006647
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000004728
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1420
TTAGAAAATGGAGAGGCAGAAATGTCCCCAGAAGAATCATGGGAGCACAAACAAGAACCTAGTGAAGCAGAGCCAGGGGG
TGGCTCTTTGGGAGATGGAGGGCCTCCTGAGGAGAATGTCCAAGAAATGATGGAGGAGGAAGAAGAAATGCCAAAACCTA
AATCTGTGGTAGCATCACCAGGTGCACCTAAGAAAGAACATGTAAGTGTAGTATTCATTGGGCATGTAGATGCTGGTAAA
TCAACTATTGTAGGACAAATAATGTATTTGATGGGGATGGTTGACAAAAGAACACTTGAAAAATATGAACAAGAAGCTAA
AGAAAAAAACAGAAACTTGGTACTTGTCATGGGCCTTAGATACAAATTAGGAAGAACGAGACAAAGGTAAAACTGTAGAA
GTGGGCCGAGCGTACTTTGAGACAGAAAAGAAGCATTTCACCATCCTAGATGCCCCTGGGCACAAGAGTTTTGTCCCAAA
CATGATTAGTGGTGCTTCTCAAGCTGATTTGGCTGTACTGGTAATCTCTGCCTGGAAAGGAAAGTTTGAAACTGGATTTG
AAAAAGGAGGACAGACAAGAGAACATGCCATGTTGGCAAAAACAGCAGGTGTAAAATACTTAATAGTGCTTATTAATAAG
ATGGATGATCCAACAATAAATCAGAGCAATGAAAGATATGAAGAATGTAAAGAAAAGTTGGTGCCATTTTTGAAAAAAGT
TGGCTTCAATCCCAAAAAGGATATTCACTTCATTCCCTGCTCAGGATTGACTGGTGCAAACCTTATAGAGCAATCAGATT
TCTGTCCTTGGGATATTGGGTTACCATTTATTCCATATCTGGATAATTTGCCAAACTTCAACAGATCAGTTGATGGATCA
ATCAGGCTGCCAATTGTGGGTAAATACAAGGATATGGGCACTGTGGTTCTAGGAAAGCTGGAATCAGGCTCTATTTGCAA
AGGACAGCAGCTTGTATTGATGCCAAACAAGCACAACGTGGAAGGTCTTGGAATCCTTTCTGATGATGTAGAAACTGATT
CTGTAGCCCCAGGTAAAAACCTCAAGATTAGACTGAAGGGAATTGAAGAAGAAGAAATTCTTCCAGGATTCATACTCTGT
GATCCTAATAATCTATTCATTCAGGATACACATTTGATGCCCAG

ORF - retro_mdom_1420 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.79 %
Parental protein coverage: 66.38 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVENGETEMSPEESWEHKEEPSEAEPRGGSSGDGGPPEESVQEMMEEEEEIPKPKSVVAPPGAPKKEHVNV
.ENGE.EMSPEESWEHK.EPSEAEP.GGS.GDGGPPEE.VQEMMEEEEE.PKPKSVVA.PGAPKKEHV.V
RetrocopyLENGEAEMSPEESWEHKQEPSEAEPGGGSLGDGGPPEENVQEMMEEEEEMPKPKSVVASPGAPKKEHVSV
ParentalVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYE-REAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAY
VFIGHVDAGKSTI.GQIMYL.GMVDKRTLEKYE....K.K..ETWYLSWALDTN.EERDKGKTVEVGRAY
RetrocopyVFIGHVDAGKSTIVGQIMYLMGMVDKRTLEKYE>KKLKKKT-ETWYLSWALDTN*EERDKGKTVEVGRAY
ParentalFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLI
FETEKKHFTILDAPGHKSFVPNMI.GASQADLAVLVISA.KG.FETGFEKGGQTREHAMLAKTAGVK.LI
RetrocopyFETEKKHFTILDAPGHKSFVPNMISGASQADLAVLVISAWKGKFETGFEKGGQTREHAMLAKTAGVKYLI
ParentalVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDIHFMPCSGLTGANLKEQSDFCPWYIGLPFIP
VLINKMDDPT.N.SNERYEECKEKLVPFLKKVGFNPKKDIHF.PCSGLTGANL.EQSDFCPW.IGLPFIP
RetrocopyVLINKMDDPTINQSNERYEECKEKLVPFLKKVGFNPKKDIHFIPCSGLTGANLIEQSDFCPWDIGLPFIP
ParentalYLDNLPNFNRSVDGPIRLPIVDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDSV
YLDNLPNFNRSVDG.IRLPIV.KYKDMGTVVLGKLESGSICKGQQLV.MPNKHNVE.LGILSDDVETDSV
RetrocopyYLDNLPNFNRSVDGSIRLPIVGKYKDMGTVVLGKLESGSICKGQQLVLMPNKHNVEGLGILSDDVETDSV
ParentalAPGENLKIRLKGIEEEEILPGFILCDPNNL-CHSGRTFDAQ
APG.NLKIRLKGIEEEEILPGFILCDPNNL..HSG.TFDAQ
RetrocopyAPGKNLKIRLKGIEEEEILPGFILCDPNNL<IHSGYTFDAQ

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_1420 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1420 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 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095891 retrocopy
retro_amel_4,
Bos taurus ENSBTAG000000035772 retrocopies
retro_btau_1793, retro_btau_1840,
Canis familiaris ENSCAFG000000188561 retrocopy
retro_cfam_2072,
Callithrix jacchus ENSCJAG000000181911 retrocopy
retro_cjac_618,
Cavia porcellus ENSCPOG000000093811 retrocopy
retro_cpor_73,
Equus caballus ENSECAG000000211951 retrocopy
retro_ecab_739,
Echinops telfairi ENSETEG000000182491 retrocopy
retro_etel_1626,
Felis catus ENSFCAG000000222811 retrocopy
retro_fcat_1913,
Gorilla gorilla ENSGGOG000000040711 retrocopy
retro_ggor_2906,
Microcebus murinus ENSMICG000000141371 retrocopy
retro_mmur_28,
Myotis lucifugus ENSMLUG000000007921 retrocopy
retro_mluc_98,
Macaca mulatta ENSMMUG000000231781 retrocopy
retro_mmul_118,
Monodelphis domestica ENSMODG00000004728 1 retrocopy
retro_mdom_1420 ,
Mustela putorius furoENSMPUG000000145041 retrocopy
retro_mputfur_147,
Mus musculus ENSMUSG000000622031 retrocopy
retro_mmus_238,
Nomascus leucogenys ENSNLEG000000101991 retrocopy
retro_nleu_2705,
Oryctolagus cuniculus ENSOCUG000000047591 retrocopy
retro_ocun_1664,
Otolemur garnettii ENSOGAG000000070831 retrocopy
retro_ogar_100,
Pteropus vampyrus ENSPVAG000000050091 retrocopy
retro_pvam_1426,
Rattus norvegicus ENSRNOG000000023351 retrocopy
retro_rnor_2931,
Sarcophilus harrisii ENSSHAG000000059081 retrocopy
retro_shar_14,
Ictidomys tridecemlineatus ENSSTOG000000154061 retrocopy
retro_itri_109,
Tupaia belangeri ENSTBEG000000088732 retrocopies
retro_tbel_3810, retro_tbel_4659,
Tarsius syrichta ENSTSYG000000138122 retrocopies
retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus ENSTTRG000000116301 retrocopy
retro_ttru_12,


Copyright © RetrogeneDB 2014-2017