RetrogeneDB ID: | retro_mdom_1049 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:379168602..379169935(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HSPH1 | ||
| Ensembl ID: | ENSMODG00000009347 | ||
| Aliases: | None | ||
| Description: | heat shock 105kDa/110kDa protein 1 [Source:HGNC Symbol;Acc:16969] |
Retrocopy-Parental alignment summary:
>retro_mdom_1049
GGTGTTCATGAAGTATTCAGCTGGAACCATGCTGCTCCTTTCTCCAAAGTTCTCACTTTTTATAAGAAAGGTCCCTTTCA
GTTGGAAGCTTTGTACTCTGATCCTGAAGGCTTTCCATACCCAGAAGCAAAAATTGGCTGCTTTGTAGTCCAAAATGTTT
CAGCTCAGAAAGATGGCGAGAAATCTAAAGTCAAAGGTAAAGTACGGCTCAACACTCATGGCATTTTTACAATATCTACT
GCATCAATGGTGGAGAAAATCCCAACAGAAGAAAGTGAGGGTTCCTCCATTGAAACACATATGGAGCATCAGAGCCGACC
CCCACCTGAAACCACTGACTTGGATAAAAATATCCAGCAAGACAACAGTGAAGCTGGAACACAGCCCCAGGTACAAACTG
ATGGTCAGCAAACTCCACAGTGTCCCCCTTCACCTGACCTTCCCTCTGAAGAAAAGAAAATCCCTGACACTGACAAAGCA
AATAAAAAGAAAGGAGATCAACCTCCAGAAACTAAAAAACCCAAAATAAATGTGGTGAATGTTGAACTTCTCATTGAAGC
AAACTTGGTCTGGCAATTGGGAAAAGACCTTTTCAAAATGTATTTTGAGACAGAAGGCAAAATGATCATGCAAGACAAGC
TAGATAAAGAAAGGAATGATGCCAAAAAATGCAGTTGAAGAATATGTCTATGAATTCAGGGATAAGCTATCTGGGCCTTA
TGAAAAGTTTGTATGTGAACAGGATCATCAAAATTTCCTGAAACTCTTAACAGAAGCTAAAGATTGGCTATATGAGGAGG
GAGAGGACCAAGCCAAATAAGCATATGTTGACAAGTTGGACCAGTTAATGAAATTAGGCACTCCCATTAAGATTAGGTTT
CAAGAAGCTGAGGAAAGACCAAGAATGTTTGAAGAGTTAGGACTAAAGCTGCAACACTATGCAAAAATAGCTGGTGACTA
CAGGAATAAAGATGAGAGGTACATCCATATTGATGAATCTGAAATGAAGAAAGTTGAAAAATCTGTCAATGAAACAATGG
AGCAGATGAATAATGTCATGAATGCCCAAGCTAAAAGAAGCCTTGATGGGATCCACTTGTATGTGGCAATGAAATTAAAA
TGAAGGTGGAGGAATTAATCCATGTTTGTGAACCAGTTGTGACACAGCCGAAACCAAAAGTAGAATCTCCCAAGCAGGAA
AAAAACACTCAATGGCCCCAACATGGATAAGAATGAAGGGTTTGAAGTAAAAAATAACCCAAATGCTGAGGGCCTGCATC
AGAATGGAGTCTGTCACCCCAGTGAGAACAGCAGCATTCATATGGATTTGGAC
ORF - retro_mdom_1049 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.06 % |
| Parental protein coverage: | 54.95 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GVHEVFSRNHAAPFSKVLTFYRKGPFELEAFYSDPEGFPYPEAKIGRFVVQNVSAQKDGEKSKVKVKVRV |
| GVHEVFS.NHAAPFSKVLTFY.KGPF.LEA.YSDPEGFPYPEAKIG.FVVQNVSAQKDGEKSKVK.KVR. | |
| Retrocopy | GVHEVFSWNHAAPFSKVLTFYKKGPFQLEALYSDPEGFPYPEAKIGCFVVQNVSAQKDGEKSKVKGKVRL |
| Parental | NTHGIFTISTASMVEKIPTEESEGSSIETDMEHQSRPPPETTDVDKNIQQDNSEAGTQPQVQTDGQQTPQ |
| NTHGIFTISTASMVEKIPTEESEGSSIET.MEHQSRPPPETTD.DKNIQQDNSEAGTQPQVQTDGQQTPQ | |
| Retrocopy | NTHGIFTISTASMVEKIPTEESEGSSIETHMEHQSRPPPETTDLDKNIQQDNSEAGTQPQVQTDGQQTPQ |
| Parental | CPPSPDLPSEENKIPDADKANEKKGDQPPEAKKPKIKVVNVELPIEANLVWQLGKDLLNMYIETEGKMIM |
| CPPSPDLPSEE.KIPD.DKAN.KKGDQPPE.KKPKI.VVNVEL.IEANLVWQLGKDL..MY.ETEGKMIM | |
| Retrocopy | CPPSPDLPSEEKKIPDTDKANKKKGDQPPETKKPKINVVNVELLIEANLVWQLGKDLFKMYFETEGKMIM |
| Parental | QDKLEKERNDA-KNAVEEYVYEFRDKLSGPYEKFVCEQDHQNFLKLLTETEDWLYEEGEDQAKQAYVDKL |
| QDKL.KERNDA.KNAVEEYVYEFRDKLSGPYEKFVCEQDHQNFLKLLTE..DWLYEEGEDQAK.AYVDKL | |
| Retrocopy | QDKLDKERNDA>KNAVEEYVYEFRDKLSGPYEKFVCEQDHQNFLKLLTEAKDWLYEEGEDQAK*AYVDKL |
| Parental | DQLMKLGTPIKIRFQEAEERPRMFEELGLKLQHYAKIAGDYRNKDERYIHIDESEMKKVEKSVNETMEWM |
| DQLMKLGTPIKIRFQEAEERPRMFEELGLKLQHYAKIAGDYRNKDERYIHIDESEMKKVEKSVNETME.M | |
| Retrocopy | DQLMKLGTPIKIRFQEAEERPRMFEELGLKLQHYAKIAGDYRNKDERYIHIDESEMKKVEKSVNETMEQM |
| Parental | NNVMNAQAKRSLD-QDPVVCGNEIKMKVEELIHVCEPVVTQPKPKVESPKQE-KTLNGPNVEKNEGFEVK |
| NNVMNAQAKRSLD..DP.VCGNEIKMKVEELIHVCEPVVTQPKPKVESPKQE.KTLNGPN..KNEGFEVK | |
| Retrocopy | NNVMNAQAKRSLD<WDPLVCGNEIKMKVEELIHVCEPVVTQPKPKVESPKQE>KTLNGPNMDKNEGFEVK |
| Parental | NNPNAEGLHQNGDCHPSENSSIHMDLD |
| NNPNAEGLHQNG.CHPSENSSIHMDLD | |
| Retrocopy | NNPNAEGLHQNGVCHPSENSSIHMDLD |
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_1049 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1049 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000013998 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000009347 | 1 retrocopy |
retro_mdom_1049 ,
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