RetrogeneDB ID: | retro_mdom_549 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:267858368..267859632(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FTO | ||
| Ensembl ID: | ENSMODG00000009684 | ||
| Aliases: | None | ||
| Description: | fat mass and obesity associated [Source:HGNC Symbol;Acc:24678] |
Retrocopy-Parental alignment summary:
>retro_mdom_549
ATGAAATGAAGTGAAAGCACCTGTGACCCAGAGCAGGAAGCAAAGAAGCAGAAGCTTCTTAAAGAACTTGGAAAAAGATG
ACTTCCTTATCTAAGCCCCAAAGATACTGAATTCCACTAGCTGTGGCAGGAGAATTATTCCAAACTGATTCTCCAAGAAG
CCAGTAGCATCCCATAATTGTTGCATAAGGAAGTTCAGCAAGCCTTCCTCATCTTGCGCAGGCATGGCTGCTTATTCCAG
GATCTAGTCCGAATCAAAGGGAAAAATTTACTCACACCAGTGTCTTACCTTCTTATTGGAAATCCAAGGTACACTTATAA
GTATCTGAATAGCAGACTCTTCACTGTGCCATGGACGATGGAAAGTTCCAACATAAAATATTCCAAAGTTGAAATATTTG
CAGCTTGTAGAGCCTTCTTGAAGCTTAATGACTACTTGCATAAAGATACAATTCAAGTTTTGGACAAACTACACTTCATA
AAATCCAAGGACAGTGAAGACAGTGCAGTCTTTGGCATGGTCCCAGAACTCTCCAAGAACACTTTGAATGTGGGACATGA
TATGGAACTTAAGAAGAGGACAACTTACAATTTGACCTTGTTGAATTACATGGATCCTCAAGAAATGTCTTACTTGAAAG
AAGAACCTTATTTTGGGATGGGAAAAATGGCTGTGAGCTGGCGTCATGATGAGAACCTAGTAGAAAGGTCCACAGTGGCT
GTATACAGTTACAATTATGAAGGCCCGGAAGTTCTTGATGATGGTGAGCTGAGTCCAGAAGGGAGAAACTCCGCTGTCTA
GCATGTTGGTCTGAAGATAGCTTGGGACATAAAGACACCTGGTTTAGCTGTACCCCTCCATCAAGGAGACTGCTGTCATA
TGCTAGACAATCTTAATTCAACCCATCAACACTGTGTTTTGGCCAGTTGGCAACCTCGATTCAGTTCCACCCACAGAGTG
GCTGAGCATTCAATAGGGACTCTGGATTATATTTTTAAGCAATGCCACTTGGCACTTCAGAATGTAAAAGATGACACGGA
GCCCAGAACTGTGCATTTGAGATCCATGGAGTCATCAGTTATCAAGCAGGGGGAAGAAATTCATAATGAGGTAGAATTTG
AATGGGCTGAGACAGTTTTGGTTTCATGGCCATCGCTATAAGAAGAGCACAGATTGGTGGCAGCTACCCATGTCTGAACT
GGAAGGATTGTGGAAAAAGATGGAATGTGTGACAAATGCAGTGCTTGGTGAATTCAGAACAGAG
ORF - retro_mdom_549 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.47 % |
| Parental protein coverage: | 89.01 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MKRRESTCDPEREAKKQKLLKELGNRWLPYLTPKDTEFHQLWQENYSKLILREASSIPELLHKEVQQAFL |
| MK..ESTCDPE.EAKKQKLLKELG.R.LPYL.PKDTEFH.LWQENYSKLIL.EASSIP.LLHKEVQQAFL | |
| Retrocopy | MK*SESTCDPEQEAKKQKLLKELGKR*LPYLSPKDTEFH*LWQENYSKLILQEASSIP*LLHKEVQQAFL |
| Parental | ILRKHGCLFQDLVRIKGKNLLTPVSRLLIGNPGYTYKYLNSRLFTVPWPMEGSNIKYSKDEIFAACRAFF |
| ILR.HGCLFQDLVRIKGKNLLTPVS.LLIGNP.YTYKYLNSRLFTVPW.ME.SNIKYSK.EIFAACRAF. | |
| Retrocopy | ILRRHGCLFQDLVRIKGKNLLTPVSYLLIGNPRYTYKYLNSRLFTVPWTMESSNIKYSKVEIFAACRAFL |
| Parental | KLNDYLRKDTIQALDKLHLIKSKDSEDSAVFGMVPELSKNILNVGHDMELKKRTTYNLTLLNYMDPQEMS |
| KLNDYL.KDTIQ.LDKLH.IKSKDSEDSAVFGMVPELSKN.LNVGHDMELKKRTTYNLTLLNYMDPQEMS | |
| Retrocopy | KLNDYLHKDTIQVLDKLHFIKSKDSEDSAVFGMVPELSKNTLNVGHDMELKKRTTYNLTLLNYMDPQEMS |
| Parental | YLKEEPYFGMGKMAVSWHHDENLVERSTVAVYSYNCEGPEVLDDDELSPEGRNPAVWHVGLKIAWDIKTP |
| YLKEEPYFGMGKMAVSW.HDENLVERSTVAVYSYN.EGPEVLDD.ELSPEGRN.AV.HVGLKIAWDIKTP | |
| Retrocopy | YLKEEPYFGMGKMAVSWRHDENLVERSTVAVYSYNYEGPEVLDDGELSPEGRNSAV*HVGLKIAWDIKTP |
| Parental | GLAVPLHQGDCYLMLDNLNSTHQHCVLAGLQPRFSSTHRVAECSAGTLDYIFKQCHLALQNVKDDTEPRT |
| GLAVPLHQGDC..MLDNLNSTHQHCVLA..QPRFSSTHRVAE.S.GTLDYIFKQCHLALQNVKDDTEPRT | |
| Retrocopy | GLAVPLHQGDCCHMLDNLNSTHQHCVLASWQPRFSSTHRVAEHSIGTLDYIFKQCHLALQNVKDDTEPRT |
| Parental | VHLRSMESSVIKQGEEIHNEVEFEW-LRQFWFHGHRYKKCTDWWQLPMSELEGLWKKMECVTNAVLDEIR |
| VHLRSMESSVIKQGEEIHNEVEFEW.LRQFWFHGHRYKK.TDWWQLPMSELEGLWKKMECVTNAVL.E.R | |
| Retrocopy | VHLRSMESSVIKQGEEIHNEVEFEW>LRQFWFHGHRYKKSTDWWQLPMSELEGLWKKMECVTNAVLGEFR |
| Parental | KE |
| .E | |
| Retrocopy | TE |
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 | 13 .83 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 16 .65 RPM |
| SRP007412_heart | 0 .00 RPM | 14 .75 RPM |
| SRP007412_kidney | 0 .00 RPM | 31 .60 RPM |
| SRP007412_liver | 0 .00 RPM | 7 .55 RPM |
| SRP007412_testis | 0 .00 RPM | 31 .43 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_549 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_549 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 | ENSMODG00000009684 | 1 retrocopy |
retro_mdom_549 ,
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