RetrogeneDB ID: | retro_mdom_423 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:480153004..480154017(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FSCN1 | ||
| Ensembl ID: | ENSMODG00000001028 | ||
| Aliases: | None | ||
| Description: | fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus) [Source:HGNC Symbol;Acc:11148] |
Retrocopy-Parental alignment summary:
>retro_mdom_423
TCTTGCTTCACGCAGGCATCTCACTCGCTGAGAAGTTAAGTGTCCTCATCACCATGGTCCTGCAGGTGAACCTCTACAAA
CTGACCCCCAAGTGCTAGGGGCACCTGAGCCCCAGGAAGGATAAGATCGCTGTGGACATCGACGTGCCCTGGGGAGTGGA
CTCATTCATTACCCTGGTCTTCCAGGACTAGCCCTACCATGTGCCAACTGCGACTACTGTTTCCTGCGCAACAATGGGCA
CCTGGTGGAAAGACCTGAGAGGGGCACGATCTACATCCTGTAGTTCAGATCTGGCAAAGTGGCTTTCAGGGACTTCAAGG
ACCATTACCAGGAGCCAGTTGAACCCAACAGCACTCTTAAGGCAGGCATGAGCACCAAGATGGGCGAGATATACTCTTCT
TACTAGAACAGAATTGTCCCAAGGTGGTACTGCAGGAAGACAACCAGAGGAACATGTATGCTGGGCAGAAAATAGACCTC
TCTGCCAATTGGGATGAAGAGAGTGACTTAGAAATTTTCCCACTAGAGATCAATAGAGACACCAATAAATGTGCTCTCTG
GAGCAATACTGACAAATACTGGACCCTAACATTCAGTGGTGGCATACTTGTCCACTGCTTCGACCAAGACCGCCAACTAC
TGCTTTGACATAGAATGGTGTGACAAAGGCATCACTGTCAAAACTGCCAATGAGAAGTAGGTTACAACCTCAGAAAAATG
GAGAACTGGTGGCCTCTTTGGAAGCTGCAAAAGAAAATCGGCATTTGTTAAAATTGATCAAGAGACCCATCATCTTGTTC
TCAGGAATCTATGGCTTCATTGGATGCTAGAGAGTGAGTGGGATGGTGGATTCAGATTGCTCTTCATTCCAGTTGGAAGT
TAATAGTTGTGTCTACAATATCAAAGACTCTACTGGGAAGTATTGGATGATGGGAAATGAATCATCTATCATCAGTAGCA
GCAAAATTCCCAGAGACTTCTTTTTCAAGTTCTGTGACCATGACAAAGTAGCC
ORF - retro_mdom_423 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.84 % |
| Parental protein coverage: | 69.23 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | SCFAQT-ISPAEKWSVHIAMHPQVNIYSLTRKRYAHLSARQDEIAVDRDVPWGVDSLITLVFQDQRYSVQ |
| SCF.Q..IS.AEK.SV.I.M..QVN.Y.LT.K...HLS.R.D.IAVD.DVPWGVDS.ITLVFQD..Y.V. | |
| Retrocopy | SCFTQA<ISLAEKLSVLITMVLQVNLYKLTPKC*GHLSPRKDKIAVDIDVPWGVDSFITLVFQD*PYHVP |
| Parental | TA-DHRFLRNDGRLVESPEPGTGYTLEFRSGKVAFRDCEGRYLAPSGPSGTLKAGKSTKVG-KDELFVLE |
| TA.D..FLRN.G.LVE.PE.GT.Y.L.FRSGKVAFRD....Y..P..P..TLKAG.STK.G..D.LF.LE | |
| Retrocopy | TA<DYCFLRNNGHLVERPERGTIYIL*FRSGKVAFRDFKDHYQEPVEPNSTLKAGMSTKMG<RDILFLLE |
| Parental | QSCPQVVLQAGNQRNVSTRQGMDLSANQDEESDQETFQLEINRDTKKCAFRTHTGKYWTLTSNGGI-QST |
| Q.CP.VVLQ..NQRN....Q..DLSAN.DEESD.E.F.LEINRDT.KCA....T.KYWTLT..GGI..ST | |
| Retrocopy | QNCPKVVLQEDNQRNMYAGQKIDLSANWDEESDLEIFPLEINRDTNKCALWSNTDKYWTLTFSGGI>LST |
| Parental | ASTKNASCYFDIEWCDKRITLKAANGKYVTA-KKNGQLAASVEAAGETEHFLMKLINRPIIVFRGEHGFI |
| ASTK.A...FDIEWCDK.IT.K.AN.K.VT...KNG.L.AS.EAA.E..H.L.KLI.RPII.F.G..GFI | |
| Retrocopy | ASTKTANYCFDIEWCDKGITVKTANEK*VTT>QKNGELVASLEAAKENRH-LLKLIKRPIILFSGIYGFI |
| Parental | GCRKVTGTLDSNRSSYDVFQLEFNDGAYNIKDSTGKYWMVGNESSVTSSSNTPVDFFFEFCDYNKVA |
| GC..V.G..DS..SS...FQLE.N...YNIKDSTGKYWM.GNESS..SSS..P.DFFF.FCD..KVA | |
| Retrocopy | GC*RVSGMVDSDCSS---FQLEVNSCVYNIKDSTGKYWMMGNESSIISSSKIPRDFFFKFCDHDKVA |
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 | 6 .88 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_423 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_423 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 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000075618 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000001028 | 1 retrocopy |
retro_mdom_423 ,
|
| Ornithorhynchus anatinus | ENSOANG00000030243 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017337 | 3 retrocopies |