RetrogeneDB ID: | retro_mdom_2009 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | X:15471858..15473193(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FXR2 | ||
| Ensembl ID: | ENSMODG00000007179 | ||
| Aliases: | None | ||
| Description: | fragile X mental retardation, autosomal homolog 2 [Source:HGNC Symbol;Acc:4024] |
Retrocopy-Parental alignment summary:
>retro_mdom_2009
CGGCTAGCAGCTGCATTCCAAGACGAATTTACAGTACAGGAAGACCTAATGGGATTAGCAATTGGAACTCTTGGTGCCAA
TATTCAGTAGGCCCAAAAAGTGCCTGGGGTGACAGTCATTGAACTGGTCGAGGAGACTTGCACCTTCTGAATCTACAGGA
AGACCCCTGAAGCATGCCGGTAGGCCCAAATCTACCTAGAGTTTTCCGAAGACTCTGTCCAAGTGCCCTGGAACCTGGTT
GGAAAAGAGATTAAGAAGAATGGGAAAGTGATCCAGGAGATTGTGGATAAATCTGGTGTGGTGAGGTTTCGAGTGGAGGG
TGGTAATGACAAGAAGAATCCAAGGGAGGAGGGAATGGTTCCTTTCACATTTGTTGGTACCTGGGAGAACATCAGCAATG
CTCAGGCCCTACTGGAATATCACCTCTCTTACTTGCAGCAAGTAGAACAGTTTCAATTAGAAAGACTACTGATTGATGAA
CAACTTCAGCAGATTGGGCTGGGCTTCTGTACCCCTGGAACTGATCGAGGAAACAGTAGTGGTGACAAGACTGGCTACGC
CACAGATGAAAGCTCTTCCTCTTCCCTCCATGCCACTAGTTCCTATGGGGATTGTGGCCATGGCCGGAAGACAGGAAGTT
CTGGCTATGGCCCTGGTTCAGATCGGTCCACTGCTTCTGAAACTGAGTCTGAGAAACAAGAGGAGCCTGACCAGTCTGCA
CATGGTGAGCAGGGTTCCTCTAGACTTGGTGAAAAGGATCGTAGGAGACCAATGGGGGTCCGAGGTCGAGGGTCTAATCC
TAAACCTCGGCTTCCTAGCAAGGATACAACACCTTCCATTATCTCAGTGCTGAAGGATCCTGACAGTAATCCCTACTGCC
TACTGGACACATCAGAACCAGAGCCCCCAGTTGACTCTGAGCCTGAAGAGCCACCTCCAGCTATTGCCCATCAACGACAT
TCCCTCCATCACCATAGAGATGAGGATCGGACCATCATAGATGGAGGACTGGAATCTGATGGCCCTAATCTGGCTGAAAA
TGGTCTGGAAGAATAATCAAAACCCCAATGACTCAACAGAAGCCATAGATGACATAAATGTGGTAACCAAGCAGATGACT
CCATCAGCAGAGATCGGCAGCCAGTGACAGTGGCAGATTACATCTCCTAGGCAGAATCTCAGAGCCGACAGAGGCAGCCC
CCTGATCCCACTCATGTTCCTTCCGAGGACTCTCTCTCAAGACCAAAGGGTGTCAGCAAGCTTTCTAAGGGCCCCTCGGA
AAATGGAGAGTTCTCTGCCTCCTTGGAGCTGGGCAGCTTGGTGAATGGGATCTCA
ORF - retro_mdom_2009 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.25 % |
| Parental protein coverage: | 77.66 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QLAAAFQEEFTVREDLMGLAIGTHGANIQQARKVPGVTAIELGEETCTFRIYGETPEACRQARSYLEFSE |
| .LAAAFQ.EFTV.EDLMGLAIGT.GANIQ.A.KVPGVT.IEL.EETCTF.IY..TPEACR.A..YLEFSE | |
| Retrocopy | RLAAAFQDEFTVQEDLMGLAIGTLGANIQ*AQKVPGVTVIELVEETCTF*IYRKTPEACR*AQIYLEFSE |
| Parental | DSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKNPREEGMVPFIFVGTRENISNAQALLEY |
| DSVQVP.NLVGK.I.KNGKVIQEIVDKSGVVR.RVEG.NDKKNPREEGMVPF.FVGT.ENISNAQALLEY | |
| Retrocopy | DSVQVPWNLVGKEIKKNGKVIQEIVDKSGVVRFRVEGGNDKKNPREEGMVPFTFVGTWENISNAQALLEY |
| Parental | HLSYLQEVEQLRLERLQIDEQLRQIGLGFRTPGSGRGNSSGDKTGYATDESSSSSLHATRTYGGRGRGRR |
| HLSYLQ.VEQ..LERL.IDEQL.QIGLGF.TPG..RGNSSGDKTGYATDESSSSSLHAT..YG..G.GR. | |
| Retrocopy | HLSYLQQVEQFQLERLLIDEQLQQIGLGFCTPGTDRGNSSGDKTGYATDESSSSSLHATSSYGDCGHGRK |
| Parental | TGSSGYGPGSDLSTASETESEKREEPDRPGHGDQDTSSRGEEGRRRPMGGRGRGSNPAPRLPSKYTTSSI |
| TGSSGYGPGSD.STASETESEK.EEPD...HG.Q..S..GE..RRRPMG.RGRGSNP.PRLPSK.TT.SI | |
| Retrocopy | TGSSGYGPGSDRSTASETESEKQEEPDQSAHGEQGSSRLGEKDRRRPMGVRGRGSNPKPRLPSKDTTPSI |
| Parental | SSVLKDPDSNPYSLLDTSEPEPPVDSEPGEPPPASARRRRSRRRRTDEDRTIIDGGLESDGPNLAENGLE |
| .SVLKDPDSNPY.LLDTSEPEPPVDSEP.EPPPA.A..R.S.....DEDRTIIDGGLESDGPNLAENGLE | |
| Retrocopy | ISVLKDPDSNPYCLLDTSEPEPPVDSEPEEPPPAIAHQRHSLHHHRDEDRTIIDGGLESDGPNLAENGLE |
| Parental | EESKPQRRNRSRRRRNRGNRADGSISRDRQPVTVADYISRAESQSRQRQPPEPTHVPSEDSLSGPKGVSK |
| E.SKPQ..NRS.R....GN.AD.SISRDRQPVTVADYIS.AESQSRQRQPP.PTHVPSEDSLS.PKGVSK | |
| Retrocopy | E*SKPQ*LNRSHR*HKCGNQADDSISRDRQPVTVADYIS*AESQSRQRQPPDPTHVPSEDSLSRPKGVSK |
| Parental | LPKGPSENGELSASLELGSLVNGVS |
| L.KGPSENGE.SASLELGSLVNG.S | |
| Retrocopy | LSKGPSENGEFSASLELGSLVNGIS |
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_2009 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_2009 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 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000018613 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000007179 | 1 retrocopy |
retro_mdom_2009 ,
|
| Rattus norvegicus | ENSRNOG00000011876 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000015678 | 1 retrocopy |