RetrogeneDB ID: | retro_mdom_700 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 2:157266451..157266966(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CA10 | ||
| Ensembl ID: | ENSMODG00000012548 | ||
| Aliases: | None | ||
| Description: | carbonic anhydrase X [Source:HGNC Symbol;Acc:1369] |
Retrocopy-Parental alignment summary:
>retro_mdom_700
GTTCAGCTAATCCACTATAACCATGAGTTATATACAAATGTCACAGAGGCTGCAAAAAGTCCAAATGGATTGGTAGTAGT
TTCTACATTTATGAAAGTTTCTGATCAAATCCATTTCTTAATCGAATGCTCAACAGAGATACCATCACAAGAATAACGTA
TAAAAATGATGCATGCTTGCTTCAGGGACTTAATATAGAGGAACTATATCCTGAGACCTCTAGCTTCATTACCTACGATG
GGTCAATGACTATCCCACCCTGTTATGAGGCAGCAAGTTGGATAATAATGAACAAACCAGTCTACATAACCAGGATGCAG
ATGTATTCCTTATGACTGCTCAGCCAGAATCAGCCATCTCAGATCTTTCTGAGCATGAGTGACAACTTCCAGCCTGTTCA
GCCACTCAATAACCGTTGCATCCGTACCAACATCAACTTTAGTTTACAAGGGAAAGACTGTCCAAATAACAGAGCCCAGA
AGCTACAATATAGAGTAAACGAATGGCTGCTCAAG
ORF - retro_mdom_700 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.95 % |
| Parental protein coverage: | 56.17 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VQLIHYNHELYTNVTEAAKSPNGLVVV-SIFMKVSDSSNPFLNRMLNRDTITRITYKNDAYLLQGLNIEE |
| VQLIHYNHELYTNVTEAAKSPNGL.VV.S.....S..SNPFLNRMLNRDTITRITYKNDA.LLQGLNIEE | |
| Retrocopy | VQLIHYNHELYTNVTEAAKSPNGL-VV<SFYIYESF*SNPFLNRMLNRDTITRITYKNDACLLQGLNIEE |
| Parental | LYPETSSFITYDGSMTIPPCYETASWIIMNKPVYITRMQMHSLRLLSQNQPSQIFLSMSDNFRPVQPLNN |
| LYPETSSFITYDGSMTIPPCYE.ASWIIMNKPVYITRMQM.SL.LLSQNQPSQIFLSMSDNF.PVQPLNN | |
| Retrocopy | LYPETSSFITYDGSMTIPPCYEAASWIIMNKPVYITRMQMYSL*LLSQNQPSQIFLSMSDNFQPVQPLNN |
| Parental | RCIRTNINFSLQGKDCPNNRAQKLQYRVNEWLLK |
| RCIRTNINFSLQGKDCPNNRAQKLQYRVNEWLLK | |
| Retrocopy | RCIRTNINFSLQGKDCPNNRAQKLQYRVNEWLLK |
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_700 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_700 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000009007 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000010755 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000012548 | 1 retrocopy |
retro_mdom_700 ,
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