RetrogeneDB ID: | retro_mdom_1005 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:189847967..189848693(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SRSF12 | ||
| Ensembl ID: | ENSMODG00000018282 | ||
| Aliases: | None | ||
| Description: | serine/arginine-rich splicing factor 12 [Source:HGNC Symbol;Acc:21220] |
Retrocopy-Parental alignment summary:
>retro_mdom_1005
ATGCCTCGATACACCAGGCCCCCCAACACCTCCCTTTTCGTCAGGAACGTCAGGGATACCACCAGACCTGAGGACTTGCA
ATGTGAATTTGGTCGATATGGCCCTATAGTAGACGTACACATTCCACTTGACTTCTACACTCGCTGCCCAAGAGGATTTG
CTTACTTACAATTTGAAGCTGTCTGTGATGCAGAAGATGCTCTTTATAACCTCAATAAAACGTGGGTATGTGGTCATCAA
ATTGAAATACAGTTTGCACAAGGTGATCGCAAAATACCAGGCCAAATGAAATCAAAAGAACGCCACCCTTGTTCTCCAAG
TGAACATAGAAGATCAAGAAGGCACAGTAGAAGGACTCGAAGTAGAAGTTCTTCATGGGGAAGAAGCCGGAGACAATCTG
ATAGCCTTAAAGAGTCTCCTCGTAGGGGACTTTCTTATAGCTGATCTAAATCTCGATCTAACTCATTAACAAGGCGTTCT
ACCTCAGGAAGGAAATCAAGATCTCCTAGAAGAAATTCTAGTTCTAGACGATGATCAAGATCTGAGTCCTTACAAAAAAG
GACCACATCTGTGGGAAAATCACAGTCAAGTTCACCTCAGAGGCAGACCATCTCAGGGGCAAAATCAAGATCAGGTGGAA
GACATTTTGATGTACTAGCAAGATCAAAATCTCACTAAAGACACACTAATTCTGAAACTAAAGCACAGTCTCAGAGCTAC
CATCAT
ORF - retro_mdom_1005 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.98 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSRYTRPPNTSLFVRNVTDATRPEDLRREFGRYGPIVDVYIPLDFYTRRPRGFAYLVIFEDVRDAEDALY |
| M.RYTRPPNTSLFVRNV.D.TRPEDL..EFGRYGPIVDV.IPLDFYTR.PRGFAYL..FE.V.DAEDALY | |
| Retrocopy | MPRYTRPPNTSLFVRNVRDTTRPEDLQCEFGRYGPIVDVHIPLDFYTRCPRGFAYLQ-FEAVCDAEDALY |
| Parental | NLNKKWVCGRQIEIQFAQGDRKTPGQMKSKERHPCSPSEHRRSRSHSRRTRSRSSSWGRSRRRSDSLKES |
| NLNK.WVCG.QIEIQFAQGDRK.PGQMKSKERHPCSPSEHRRSR.HSRRTRSRSSSWGRSRR.SDSLKES | |
| Retrocopy | NLNKTWVCGHQIEIQFAQGDRKIPGQMKSKERHPCSPSEHRRSRRHSRRTRSRSSSWGRSRRQSDSLKES |
| Parental | RRRGLSYSRSKSRSNSLTRHSTSGRKSRSPRRNSSSRRRSRSESLQKRTTSVGKSQSSSPQRQTTSGAKS |
| .RRGLSYS.SKSRSNSLTR.STSGRKSRSPRRNSSSRR.SRSESLQKRTTSVGKSQSSSPQRQT.SGAKS | |
| Retrocopy | PRRGLSYS*SKSRSNSLTRRSTSGRKSRSPRRNSSSRR*SRSESLQKRTTSVGKSQSSSPQRQTISGAKS |
| Parental | RSGGRHFDSLARSPSKSPQRHTNSETKAQSRSYHH |
| RSGGRHFD.LAR..SKS..RHTNSETKAQS.SYHH | |
| Retrocopy | RSGGRHFDVLAR--SKSH*RHTNSETKAQSQSYHH |
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_1005 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1005 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000014941 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000018282 | 1 retrocopy |
retro_mdom_1005 ,
|
| Tupaia belangeri | ENSTBEG00000015120 | 1 retrocopy |