RetrogeneDB ID:

retro_mdom_953

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:16796711..16798220(+)
Located in intron of:ENSMODG00000025406
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ALPL
Ensembl ID:ENSMODG00000016006
Aliases:None
Description:alkaline phosphatase, liver/bone/kidney [Source:HGNC Symbol;Acc:438]


Retrocopy-Parental alignment summary:






>retro_mdom_953
ACTATGCTTCTCCTTTTCCTGAGCCTGTTGGCTGGGGCGTGCCTCTCCTCCCTGGTCCAGGAGAAGAATCCCGAGTACTG
GAGAGCACAGGCACAGCAGACCCTCCACAAAGCCTTGGAGCTCCAGAAGCTCAACACCAACGTAGCCAAGAATGTGATCT
TGTTTGTGGGGGATGGTATGGGGGTGACCACCGTATCTGCTGCCCGGATCCTCAAAGGCCAGCTTCACCACATGCCTGGC
GAGGAGTTCCAGCTTGAAATGGAGAAGTTTCCCTTCTTGGCTCTGTCCAAGACATACAACACCAACGCCCAGGTTCCTGA
CAGTGCCGGCACAGCCACGGCCTTCCTGTGCGGGGTAAAGAGCAAAAAGGGCACCCTGGGTGTGAGTGCTGCTGCCAGCC
GATCGCAGTGCAACACCACCAAGGGCAACGAGATCACCTCAATCCTGCGCTGGGCCAAGGATGCTGGGAAGTCTGTGGGC
ATCGTGACCACCACTCGAGTGAACCACGCTACGCCCAGCGCCGCCTATGCACACTCCGTGGATAGGACATGGTATTCGGA
CAACGAGATGCCCTCCGAGGCCCTGGGCCAGGGCTGCAAGGACATAGCCCACCAGCTGATGCACAACATCCCGGATATCG
AGGTGGTCCTGGGCGGAGGCCGGAAGTACATGTTTCCTAAGGGCACACCGGATGTGGAGTACGGGAACAAGGAGGCGAGA
GGGACGAGGCTGGATGGGCAGAGACTCACCGATATCTGGAGGGAGAAGAAGCCTCCGAACAAGAATGCCTACTATGTCTG
GAACCGCAGGCAGCTGCTGAAACTGGACTGGAACCATGTGGACTTCCTTCTAGGTCTCTTCGAGCCCAAGGATATGATGT
ACGAACTTAACAGAAACCGATGGACAGACCCGTCCCTGACGGAGATGGTGGAGGTGGCCATCAAGATCCTGAGAAAGAAC
CCCGAGGGCTTTTTCCTGCTGGTAGAAGGGGGCAGAATCGACCACGGCCACCACGCGGGAAAGGCCAAACAAGCCCTCCA
CGAGGTGGTGGAGATGGACCGGGCCATCGCACGGGCTGGAGCCCTGACCTCCTCCGAGGACACGCTGACTGTGGTCACAG
CGGATCACTCCCACGTCTTCACGCTCGGTGGCCACGCTCCCCGGGGGAACTCCATCTTCGGTCTTGCCACCTCCCTGAGC
GACAGAGACAAGAAACCCTTCACTTCTCTCCTGTACGGAAATGGCCCTGGCTACAAGGTGGTGGCCGGTGAGAGGGAGAA
TGTTTTAGCTGTGGACTATGCTGATAAGAACTACCGGGCCCAGGCTGCAGTGCCCCTGAGCAAGGAAACCCACGGCAGTG
AAGACGTGCCTGTGTTCTCCAAGGGCCCCATGGCTCACCTCCTTCACGGCGTCTTCGAACAGAACTACATTCCACATGCC
ATGGCCTATGCCTCGTGCATTGGGTCCAACACAGACCACTGCCAGCCTCATTCATGATCTCAGCTAGCA

ORF - retro_mdom_953 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.8 %
Parental protein coverage: 94.92 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTMFLLLLCLMAGTCLSIVPEKEKNPWYWREQAQRTLQHSLKLQNLNTNVARNVILFLGDGMGVSTVTAAR
TM.LL.L.L.AG.CLS.....EKNP.YWR.QAQ.TL...L.LQ.LNTNVA.NVILF.GDGMGV.TV.AAR
RetrocopyTMLLLFLSLLAGACLSSLVQ-EKNPEYWRAQAQQTLHKALELQKLNTNVAKNVILFVGDGMGVTTVSAAR
ParentalILKGQLHHKLGEDFQLEMDKFPFVALSKTYNTNAQVPDSAGTATAYLCGVKSNEGTVGVSAAVTRSQCNT
ILKGQLHH..GE.FQLEM.KFPF.ALSKTYNTNAQVPDSAGTATA.LCGVKS..GT.GVSAA..RSQCNT
RetrocopyILKGQLHHMPGEEFQLEMEKFPFLALSKTYNTNAQVPDSAGTATAFLCGVKSKKGTLGVSAAASRSQCNT
ParentalTKGNEVTSILRWAKDAGKSVGIVTTTRVNHATPSAAYAHSADRDWYSDNEMPPEALNQGCKDIAYQLMHN
TKGNE.TSILRWAKDAGKSVGIVTTTRVNHATPSAAYAHS.DR.WYSDNEMP.EAL.QGCKDIA.QLMHN
RetrocopyTKGNEITSILRWAKDAGKSVGIVTTTRVNHATPSAAYAHSVDRTWYSDNEMPSEALGQGCKDIAHQLMHN
ParentalIPDIEVIMGGGRKYMFPKNTTDVEYGDDPKARGTRLDGQVLIDVWKGKKPRNKNAHYVWNRMQLMNLDLN
IPDIEV..GGGRKYMFPK.T.DVEYG....ARGTRLDGQ.L.D.W..KKP.NKNA.YVWNR.QL..LD.N
RetrocopyIPDIEVVLGGGRKYMFPKGTPDVEYGNK-EARGTRLDGQRLTDIWREKKPPNKNAYYVWNRRQLLKLDWN
ParentalNVDYLLGLFEPSDMVYELNRNNKTDPSLSEMVEVAIKILRKNPKGFFLLVEGGRIDHGHHEGKAKQALHE
.VD.LLGLFEP.DM.YELNRN..TDPSL.EMVEVAIKILRKNP.GFFLLVEGGRIDHGHH.GKAKQALHE
RetrocopyHVDFLLGLFEPKDMMYELNRNRWTDPSLTEMVEVAIKILRKNPEGFFLLVEGGRIDHGHHAGKAKQALHE
ParentalAVEMDRAIGLAGTLTSLEDTLTVVTADHSHVFTFGGYTPRGNSIFGLAPVVSDTDNKPYTSILYGNGPGY
.VEMDRAI..AG.LTS.EDTLTVVTADHSHVFT.GG..PRGNSIFGLA...SD.D.KP.TS.LYGNGPGY
RetrocopyVVEMDRAIARAGALTSSEDTLTVVTADHSHVFTLGGHAPRGNSIFGLATSLSDRDKKPFTSLLYGNGPGY
ParentalKVVAGQRENVSTVDYAHDNYQAQSAVPLSYETHGGEDVAVFAKGPMAHLLHGVQEQNYIPHVMAYASCIG
KVVAG.RENV..VDYA..NY.AQ.AVPLS.ETHG.EDV.VF.KGPMAHLLHGV.EQNYIPH.MAYASCIG
RetrocopyKVVAGERENVLAVDYADKNYRAQAAVPLSKETHGSEDVPVFSKGPMAHLLHGVFEQNYIPHAMAYASCIG
ParentalSIMDHCQSHPSAGLA
S..DHCQ.H....LA
RetrocopySNTDHCQPHS*SQLA

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_953 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_953 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000016006 1 retrocopy
retro_mdom_953 ,


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