RetrogeneDB ID: | retro_mdom_1077 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:6184766..6185567(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000025423 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GMDS | ||
| Ensembl ID: | ENSMODG00000008260 | ||
| Aliases: | None | ||
| Description: | GDP-mannose 4,6-dehydratase [Source:HGNC Symbol;Acc:4369] |
Retrocopy-Parental alignment summary:
>retro_mdom_1077
AGGGACACAGGCACTGGGGATAGTGAGATGGACAAGTCCAGGAAGGTGGCTCTCATCACCGACATCACTGGCCAGGATGG
CTCGTATTTGGCCAAATTCCTCCTGGAAAAGGGTTATGAGGTCCATGGAATCATATGTCCATCAAGTTCCTTCAACACAG
GGTGGATTGAGCATTTCTAAAAGAACCCTCAGGCTCATATTAAAGGAAATATGAAATTACATTATGGAGATATCATGGTC
AGTACCTGCCAAGTGAAGATAATTAATGAAGTGAAACCTGCAGAAAGCTACAACCTAGGAGCCCAGAGCCATGTTAAAAT
TTCTTTTGACCTTGCTGAATATACTGCTGATATTGATGGTGTCAGCACTCTATGGCTTCTTGATGCAGTCAAGACTTGTG
GCCTTATCCATTCTGTAAAGTTCCACCAAGCCTCAACAAATGAACTTTATGGAAAAGTACAAGAAATACCACAAAAGGAG
ACTACCACTTTTTATGTTCTGTCACCATATGGAGCAGCAAAACTTTATGCTAACTGGACTGTGGTGAACTTCCCTGAGAC
CTACAACCTGTTTGCTGTGAATGGCATTCTTTTCAATCATGAGAGTCCCAGAAGAGGGGCTAATTTTGTAACTCGAAAAA
TCAGCCAGTCTGTAGCTAGGATTCACCTTGGACAATTGGAGTGTTTCAGTTTGGGGAATCCGGATGCCAAGCGAGATTGG
GGCCATGCCAAGGATTATGTTGAGGCTCTGTGGCTAATGTTGCAGACTGATGAGCCAGAAGACTTTGTCATTGACTGGGG
A
ORF - retro_mdom_1077 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.39 % |
| Parental protein coverage: | 76.95 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RDPGAGDGEMGKSRKVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGN |
| RD.G.GD.EM.KSRKVALIT.ITGQDGSYLA.FLLEKGYEVHGI...SSSFNTG.IEH..KNPQAHI.GN | |
| Retrocopy | RDTGTGDSEMDKSRKVALITDITGQDGSYLAKFLLEKGYEVHGIICPSSSFNTGWIEHF*KNPQAHIKGN |
| Parental | MKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAIKTCGLINSVK |
| MKLHYGD...STC.VKIINEVKP.E.YNLGAQSHVKISFDLAEYTAD.DGV.TL.LLDA.KTCGLI.SVK | |
| Retrocopy | MKLHYGDIMVSTCQVKIINEVKPAESYNLGAQSHVKISFDLAEYTADIDGVSTLWLLDAVKTCGLIHSVK |
| Parental | FYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFV |
| F.QAST.ELYGKVQEIPQKETT.FY..SPYGAAKLYA.W.VVNF.E.YNLFAVNGILFNHESPRRGANFV | |
| Retrocopy | FHQASTNELYGKVQEIPQKETTTFYVLSPYGAAKLYANWTVVNFPETYNLFAVNGILFNHESPRRGANFV |
| Parental | TRKISRSVAKIHLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQTDEPEDFVIATG |
| TRKIS.SVA.IHLGQLECFSLGN.DAKRDWGHAKDYVEA.WLMLQTDEPEDFVI..G | |
| Retrocopy | TRKISQSVARIHLGQLECFSLGNPDAKRDWGHAKDYVEALWLMLQTDEPEDFVIDWG |
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_1077 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1077 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 | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000014600 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000008260 | 1 retrocopy |
retro_mdom_1077 ,
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