RetrogeneDB ID: | retro_mdom_679 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 2:79910628..79911876(+) | ||
| Located in intron of: | ENSMODG00000007332 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COPS3 | ||
| Ensembl ID: | ENSMODG00000004742 | ||
| Aliases: | None | ||
| Description: | COP9 signalosome subunit 3 [Source:HGNC Symbol;Acc:2239] |
Retrocopy-Parental alignment summary:
>retro_mdom_679
ATGACGTCTGCCCTGGAGCAATTCGTGAACAGCTCAATGACTCAACTTTGTGAATTGATAAACAAAAGTGGAGAACTTGC
TAGCAAAAAAAACTGATCCCACCTTGATACAGTGCTTGGTGCTTTGGATGCACCAGAGCCTTCCTTGGGGGTCCTTGCAG
TTCTGTTTGTGAAGTTTTCTATGCCCCGTGTGCCTGACTTCGAAACATTATTCTCACAGGTTCAGCTTTTTATCAGCACT
TGTAATGGGGAGCATATTAGATACTCAACAGACACTTTTGCTGGTCTTTGCCACCAGTTAACAAATACTCTCGTGGAAAG
AAAACAGCCCCTGCGAGGAATTGGTACCCTCAGACGAGCCATAGACAAGATGCAGAGGAATACAAACCAACTGACCTCAG
TCCATGCAGACCTCTGCCAGCTTTGTTTATTGGCAAAGTGCTTTAAGCCTGCCCTCCTCTATCTGGATGTGGATATGACG
GACATGTGTAAGGAGAATGGGGCTTCTGATGCAAAGCACTTCTTATGTTACTACTACTATGGTGGGATGATCTACACGGG
GCTAAAGAACTTTGAGAGAGCTCTCTACTTTTATGAGCAAGCCCTGACTACTCCTGCCATGGCACTCAGTCACATTATGC
TGGAATCCTATAAGAAGTATATTCTAGTTTCTTTGATATTACTGGGCAGAGTTCAGCAGCTGCCAAAACACACTTCTCAG
ATTGTTGGTCAATTCATTAAGCCCCTTAGCAATGCTTACCATGAACTAGCACAAGTTTATTCAACCAATAATCCATCAGA
ACTCCGAACTCTGGTAAACAAGCATAGCAAAACTTTCACTAGAGATAACAATATGGGGCTGGTTAAGCAGTGTTTTTCCT
CTATTTATAAGAAGAACATTCAGAGGCTAACAAAGACATGTTTAACGTTGTCATTACAAGACTTGGCAAGTCGTGTACAG
TTGTTAGGACCACAGGAGGCTGAAAAATATGTCCTTCACATGATAGAAGATGGTGAAATTTTTGCAAGTATTAATCAAAA
GGATGGTGTGGTCCGTTTCCATGATAATCCTGAAAAATATAACAATCCAGCTATGCTTCATAACATTGATCAGGAGGTGC
AGAAATGTATAGAGCTTGATGAGCGGCTCAAAGCCATGGATCAAGAAATCACAATGAATCCTCAGTTTGTGCAAAAGAGT
ATAGGCTCCCAAGAAGATGATTCAGAAAGCGAGCCATCCAGTTATTCT
ORF - retro_mdom_679 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.74 % |
| Parental protein coverage: | 97.65 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VNSVRQLSAQGQMTQLCELINKSGELLAKNL-SHLDTVLGALDVQEHSLGVLAVLFVKFSMPSVPDFETL |
| ..S.........MTQLCELINKSGEL......SHLDTVLGALD..E.SLGVLAVLFVKFSMP.VPDFETL | |
| Retrocopy | MTSALEQFVNSSMTQLCELINKSGELASXXX*SHLDTVLGALDAPEPSLGVLAVLFVKFSMPRVPDFETL |
| Parental | FSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRGIGILRQAIDKMQMNTNQLTSIHADLCQ |
| FSQVQLFISTCNGEHIRY.TDTFAGLCHQLTN.LVERKQPLRGIG.LR.AIDKMQ.NTNQLTS.HADLCQ | |
| Retrocopy | FSQVQLFISTCNGEHIRYSTDTFAGLCHQLTNTLVERKQPLRGIGTLRRAIDKMQRNTNQLTSVHADLCQ |
| Parental | LCLLAKCFKPALPYLDVDMMDICKENGAYDAKHFLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVS |
| LCLLAKCFKPAL.YLDVDM.D.CKENGA.DAKHFLCYYYYGGMIYTGLKNFERALYFYEQA.TTPAMA.S | |
| Retrocopy | LCLLAKCFKPALLYLDVDMTDMCKENGASDAKHFLCYYYYGGMIYTGLKNFERALYFYEQALTTPAMALS |
| Parental | HIMLESYKKYILVSLILLGKVQQLPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFT |
| HIMLESYKKYILVSLILLG.VQQLPK.TSQIVG.FIKPLSNAYHELAQVYSTNNPSELR.LVNKHS.TFT | |
| Retrocopy | HIMLESYKKYILVSLILLGRVQQLPKHTSQIVGQFIKPLSNAYHELAQVYSTNNPSELRTLVNKHSKTFT |
| Parental | RDNNMGLVKQCLSSLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGM |
| RDNNMGLVKQC.SS.YKKNIQRLTKT.LTLSLQD.ASRVQL.GPQEAEKYVLHMIEDGEIFASINQKDG. | |
| Retrocopy | RDNNMGLVKQCFSSIYKKNIQRLTKTCLTLSLQDLASRVQLLGPQEAEKYVLHMIEDGEIFASINQKDGV |
| Parental | VSFHDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGSKPSSYS |
| V.FHDNPEKYNNPAMLHNIDQE..KCIELDERLKAMDQEIT.NPQFVQKS.GSQEDDS.S.PSSYS | |
| Retrocopy | VRFHDNPEKYNNPAMLHNIDQEVQKCIELDERLKAMDQEITMNPQFVQKSIGSQEDDSESEPSSYS |
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_679 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_679 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 | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000004742 | 1 retrocopy |
retro_mdom_679 ,
|
| Nomascus leucogenys | ENSNLEG00000013466 | 1 retrocopy |