RetrogeneDB ID: | retro_dnov_2225 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_56932:239..670(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNASEH2B | ||
| Ensembl ID: | ENSDNOG00000010489 | ||
| Aliases: | None | ||
| Description: | ribonuclease H2, subunit B [Source:HGNC Symbol;Acc:25671] |
Retrocopy-Parental alignment summary:
>retro_dnov_2225
TATTTTAAAGATGCCCCAAAGAAGATGAAAAGTGGGTTTATGTTTTTAAAACTGGCTAACCCATGTTCAGGGGAAGGAGC
CGTTTACTTGTTCAACATGTGTCTACAGCAGCTGTTTGAAATAAAAGTTTTCAAGGAGCAACACCATTCTTGGTTTATAA
ATCAGTCGGTTCAATTAGAAGGTCAACTCCACTTTGCCACACCAATGGAGCCCTTATTTCTGGTTCTCCACTATCTTAAA
AAGGCTGATAAAGAGGGCAAGTTTCAGCCCCTAGATCAAGTGATGGGGATGACATGTTTCCAAATTGCACCTTGTTGCTG
AAATTTCCCGAACTGGAGAAGTTCCTTCACCATGTGACAGAGGAGAAAGAAATAGACAGCTAGAAATATTAGAAATACAG
CAAAGAGAAGACACTAAAGTGGCTGGAAAAA
ORF - retro_dnov_2225 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.1 % |
| Parental protein coverage: | 50.17 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | YFKDAPKKMKSGLMFVKLANPCSGEGAIYLFNVCLQQLFEIKVFKEKHHSWFINQSVQSEGQLHFATPMD |
| YFKDAPKKMKSG.MF.KLANPCSGEGA.YLFN.CLQQLFEIKVFKE.HHSWFINQSVQ.EGQLHFATPM. | |
| Retrocopy | YFKDAPKKMKSGFMFLKLANPCSGEGAVYLFNMCLQQLFEIKVFKEQHHSWFINQSVQLEGQLHFATPME |
| Parental | PLFLVLHYLKKADKEGKFQPLDQVV-VDDMFPNCTLLLKFPELEKFLHHVTEEKPEIDSKKYYKYSKEKT |
| PLFLVLHYLKKADKEGKFQPLDQV...DDMFPNCTLLLKFPELEKFLHHVTEEK.EIDS.KY.KYSKEKT | |
| Retrocopy | PLFLVLHYLKKADKEGKFQPLDQVM<GDDMFPNCTLLLKFPELEKFLHHVTEEK-EIDS*KY*KYSKEKT |
| Parental | LKWLEK |
| LKWLEK | |
| Retrocopy | LKWLEK |
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 |
|---|---|---|
| SRP012922_ascending_colon | 0 .58 RPM | 21 .39 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 5 .50 RPM |
| SRP012922_heart | 0 .00 RPM | 7 .19 RPM |
| SRP012922_kidney | 0 .55 RPM | 15 .06 RPM |
| SRP012922_liver | 0 .00 RPM | 3 .72 RPM |
| SRP012922_lung | 0 .00 RPM | 5 .04 RPM |
| SRP012922_quadricep_muscle | 0 .17 RPM | 6 .75 RPM |
| SRP012922_spleen | 0 .69 RPM | 18 .89 RPM |
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_2225 was not experimentally validated.
Retrocopy orthology:
Dasypus novemcinctus 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000020149 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000008585 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000010489 | 1 retrocopy |
retro_dnov_2225 ,
|
| Mus musculus | ENSMUSG00000021932 | 1 retrocopy |