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:
| Parental | TMFLLLLCLMAGTCLSIVPEKEKNPWYWREQAQRTLQHSLKLQNLNTNVARNVILFLGDGMGVSTVTAAR |
| TM.LL.L.L.AG.CLS.....EKNP.YWR.QAQ.TL...L.LQ.LNTNVA.NVILF.GDGMGV.TV.AAR | |
| Retrocopy | TMLLLFLSLLAGACLSSLVQ-EKNPEYWRAQAQQTLHKALELQKLNTNVAKNVILFVGDGMGVTTVSAAR |
| Parental | ILKGQLHHKLGEDFQLEMDKFPFVALSKTYNTNAQVPDSAGTATAYLCGVKSNEGTVGVSAAVTRSQCNT |
| ILKGQLHH..GE.FQLEM.KFPF.ALSKTYNTNAQVPDSAGTATA.LCGVKS..GT.GVSAA..RSQCNT | |
| Retrocopy | ILKGQLHHMPGEEFQLEMEKFPFLALSKTYNTNAQVPDSAGTATAFLCGVKSKKGTLGVSAAASRSQCNT |
| Parental | TKGNEVTSILRWAKDAGKSVGIVTTTRVNHATPSAAYAHSADRDWYSDNEMPPEALNQGCKDIAYQLMHN |
| TKGNE.TSILRWAKDAGKSVGIVTTTRVNHATPSAAYAHS.DR.WYSDNEMP.EAL.QGCKDIA.QLMHN | |
| Retrocopy | TKGNEITSILRWAKDAGKSVGIVTTTRVNHATPSAAYAHSVDRTWYSDNEMPSEALGQGCKDIAHQLMHN |
| Parental | IPDIEVIMGGGRKYMFPKNTTDVEYGDDPKARGTRLDGQVLIDVWKGKKPRNKNAHYVWNRMQLMNLDLN |
| IPDIEV..GGGRKYMFPK.T.DVEYG....ARGTRLDGQ.L.D.W..KKP.NKNA.YVWNR.QL..LD.N | |
| Retrocopy | IPDIEVVLGGGRKYMFPKGTPDVEYGNK-EARGTRLDGQRLTDIWREKKPPNKNAYYVWNRRQLLKLDWN |
| Parental | NVDYLLGLFEPSDMVYELNRNNKTDPSLSEMVEVAIKILRKNPKGFFLLVEGGRIDHGHHEGKAKQALHE |
| .VD.LLGLFEP.DM.YELNRN..TDPSL.EMVEVAIKILRKNP.GFFLLVEGGRIDHGHH.GKAKQALHE | |
| Retrocopy | HVDFLLGLFEPKDMMYELNRNRWTDPSLTEMVEVAIKILRKNPEGFFLLVEGGRIDHGHHAGKAKQALHE |
| Parental | AVEMDRAIGLAGTLTSLEDTLTVVTADHSHVFTFGGYTPRGNSIFGLAPVVSDTDNKPYTSILYGNGPGY |
| .VEMDRAI..AG.LTS.EDTLTVVTADHSHVFT.GG..PRGNSIFGLA...SD.D.KP.TS.LYGNGPGY | |
| Retrocopy | VVEMDRAIARAGALTSSEDTLTVVTADHSHVFTLGGHAPRGNSIFGLATSLSDRDKKPFTSLLYGNGPGY |
| Parental | KVVAGQRENVSTVDYAHDNYQAQSAVPLSYETHGGEDVAVFAKGPMAHLLHGVQEQNYIPHVMAYASCIG |
| KVVAG.RENV..VDYA..NY.AQ.AVPLS.ETHG.EDV.VF.KGPMAHLLHGV.EQNYIPH.MAYASCIG | |
| Retrocopy | KVVAGERENVLAVDYADKNYRAQAAVPLSKETHGSEDVPVFSKGPMAHLLHGVFEQNYIPHAMAYASCIG |
| Parental | SIMDHCQSHPSAGLA |
| S..DHCQ.H....LA | |
| Retrocopy | SNTDHCQPHS*SQLA |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_953 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
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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