RetrogeneDB ID: | retro_mdom_1797 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 7:149416055..149416616(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RGN | ||
| Ensembl ID: | ENSMODG00000000375 | ||
| Aliases: | None | ||
| Description: | regucalcin [Source:HGNC Symbol;Acc:9989] |
Retrocopy-Parental alignment summary:
>retro_mdom_1797
AGCAGGTGTGGAGAATTTCTAGTGTGGGAAGCAAAATCCCATAATATCCTGTTCATGAATATTCCATCCAAGAAGATTTG
CTGATGGGATTCACTCACCAATCAAGTACAAGAGGTCATATTAGATAGTCCAGTCAGCTTAGGGACCATTCAATAGTCTG
TTGGATGTATTGCAACTGTAGGGGCTCCATTTTGTTTTTTTAACTGGGAAGACCAATCACTATCTGATCTGGTTTCTATG
GATAAAGTTAAGAAAAACAATTGATTCAATTATGGGAAAATGGATTCAGCTGGGAGATACTTCCTTGGTACCTGGCCAAG
GAACCTGGCCCTGATATACTGGAGAGACAATAAGGTACCCTATATGCTCTCTTTCCTAATGGCAGTATAACAAAGAAGTA
CTTATCATGTGGACATCTCTAATGGTTTAGATTGGTCCCAGGATCACAAAAATTTCTCTTAAGTTGATAGTCTCTCTTAC
TCTGTGGATGTCTTTGATTATTATCTACAGACTGGAAAGATTACCAAATGCAGAAGTAGGTACAAGATGGAAAAAGAACA
G
ORF - retro_mdom_1797 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.9 % |
| Parental protein coverage: | 62.54 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | SRCGESPLWEEKSNSLLFVDIPGKKICRWNSLTNQVQEIVIDSPATSVAIRQCGGYVATVGTRFCVVNWE |
| SRCGE...WE.KS...LF..IP.KKIC.W.SLTNQVQE...DSP.....I....G..ATVG..FC..NWE | |
| Retrocopy | SRCGEFLVWEAKSHNILFMNIPSKKIC*WDSLTNQVQEVILDSPVSLGTIQ*SVGCIATVGAPFCFFNWE |
| Parental | NQLVSDLVSVDQDKKNNRFNDGKVDPAGRYFAGT-MAEETAPAVLERHQGSLYALFPNGTVKKYF-DNVD |
| .Q..SDLVS.D..KKNN.FN.GK.D.AGRYF.GT..A.E..P..LER..G.LYALFPNG...K.....VD | |
| Retrocopy | DQSLSDLVSMDKVKKNN*FNYGKMDSAGRYFLGT<LAKEPGPDILERQ*GTLYALFPNGSITKKY>YHVD |
| Parental | ISNGLDWSLDHKIFYYIDSLSYSVDAFDYDLQTGLIVNRRSIYKMEKEE |
| ISNGLDWS.DHK.F...DSLSYSVD.FDY.LQTG.I...RS.YKMEKE. | |
| Retrocopy | ISNGLDWSQDHKNFS*VDSLSYSVDVFDYYLQTGKITKCRSRYKMEKEQ |
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_1797 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1797 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 | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000013028 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000014821 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000000375 | 1 retrocopy |
retro_mdom_1797 ,
|
| Mustela putorius furo | ENSMPUG00000013105 | 1 retrocopy |