RetrogeneDB ID: | retro_mdom_1495 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:13436050..13436500(-) | ||
| Located in intron of: | ENSMODG00000018997 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CLTB | ||
| Ensembl ID: | ENSMODG00000005190 | ||
| Aliases: | None | ||
| Description: | clathrin, light chain B [Source:HGNC Symbol;Acc:2091] |
Retrocopy-Parental alignment summary:
>retro_mdom_1495
CTCAGCGGAGGGGGAGGAGGGGGGCAGTGCCAGCTGAAGAAGACCTAGCAGCAGCCTTCCTGGCCCAGCAGGAGAGTGAA
AACTATGATGAAGGTTTCGGAGGTGCTGAAGGAGCCCTGCAGCAACCAGTGGCTGAAAATGAGACTGGTATTGTGGACAC
GGGGGACTACAGTCAATGGAGACATGTTCCAAGAAGCCAGTGGTCCTTAAGATGGCTATGCTGCTATGGCCCAGGCAGAT
AGACTGAGTCAGGAACCAGAGAGCATCAGAAAATGGAGAGAGGAGCAGAAGAAATGGCTACAAGAACTGGATACAGCTTT
GAAAGTGACTGAGCAAGAGTGGCGGGAGAAGGCAAAGAAGGATCTGGAAGAATGGAATGTGAGACAGAATGAGCAGATGG
AGAAAAACAAAGTCAGCAACAGAGCATCAGAAGAAGCTTTCCTGAAGGAG
ORF - retro_mdom_1495 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.52 % |
| Parental protein coverage: | 68.58 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LFSSGGGPP-VPAEEDPAAAFLAQQESEIAGIENDDEGFGGAEGALQQPAAENGTGIMDMG-TTVNGDMF |
| L...GGG...VPA.E...AA....Q.......EN.DEGFGGAEGALQQP.AEN.TGI.D.G.TTVNGDMF | |
| Retrocopy | LSGGGGGGQ<VPA-EEDLAAAFLAQQES----ENYDEGFGGAEGALQQPVAENETGIVDTG>TTVNGDMF |
| Parental | QEANGPSDGYAAVAQADRLSQEPESIRKWREEQKKRLQELDAASKVTEQEWREKAKKDLEEWNVRQNEQM |
| QEA.GP.DGYAA.AQADRLSQEPESIRKWREEQKK.LQELD.A.KVTEQEWREKAKKDLEEWNVRQNEQM | |
| Retrocopy | QEASGP*DGYAAMAQADRLSQEPESIRKWREEQKKWLQELDTALKVTEQEWREKAKKDLEEWNVRQNEQM |
| Parental | EKNKVSNRIADKAFYQQ |
| EKNKVSNR....AF... | |
| Retrocopy | EKNKVSNRASEEAFLKE |
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 | 193 .69 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 255 .61 RPM |
| SRP007412_heart | 0 .00 RPM | 170 .84 RPM |
| SRP007412_kidney | 0 .00 RPM | 36 .87 RPM |
| SRP007412_liver | 0 .00 RPM | 20 .14 RPM |
| SRP007412_testis | 0 .00 RPM | 116 .68 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1495 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1495 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 | ENSMODG00000002610 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000005190 | 1 retrocopy |
retro_mdom_1495 ,
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