RetrogeneDB ID: | retro_dnov_2445 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_75405:7525..7824(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HSCB | ||
| Ensembl ID: | ENSDNOG00000011178 | ||
| Aliases: | None | ||
| Description: | HscB iron-sulfur cluster co-chaperone homolog (E. coli) [Source:HGNC Symbol;Acc:28913] |
Retrocopy-Parental alignment summary:
>retro_dnov_2445
AACTATTCCATCAGATTTGACCTCAAGAAGCTCCAGCAAAAGTGCCAGAAATCACAGCATTTTGTCCACCCAGATTTCTC
CAGCCAGAGGTCTCAGCCTGAAAAGGACTTCTCAGAGCGGCATTCAGTCTGAGCAATGATGCCTATAGGACTCTTCTAGT
TGCCCTGAGCAGGAGAAGATACCTTGTAAGTAAGTTAAAGCTCTGTGAAACAGAGATTTGAGAAGGAACGTATTATGAAA
AGGACAGCAAATTTCTCATAGAAATAGTGGAAATCAATGAAAAACTTGCAGAAGCTCAA
ORF - retro_dnov_2445 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.36 % |
| Parental protein coverage: | 62.18 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NCSFIVDTAKLQHRYQKLQRLVHPDFFSQRSQTEKDFSEKHS-RLVNDAYKTLLAPLSRGLYL---LKLH |
| N.S...D..KLQ...QK.Q..VHPDF.SQRSQ.EKDFSE.HS..L.NDAY.TLL..LSR..YL...LKL. | |
| Retrocopy | NYSIRFDLKKLQQKCQKSQHFVHPDFSSQRSQPEKDFSERHS<SLSNDAYRTLLVALSRRRYLVSKLKLC |
| Parental | GIEIHEGTDYEMDREFLMEIMEINEKLAEAQ |
| ..EI.EGT.YE.D..FL.EI.EINEKLAEAQ | |
| Retrocopy | ETEI*EGTYYEKDSKFLIEIVEINEKLAEAQ |
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 .00 RPM | 6 .81 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 3 .02 RPM |
| SRP012922_heart | 0 .00 RPM | 3 .71 RPM |
| SRP012922_kidney | 0 .00 RPM | 12 .32 RPM |
| SRP012922_liver | 0 .00 RPM | 7 .43 RPM |
| SRP012922_lung | 0 .00 RPM | 5 .35 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 4 .67 RPM |
| SRP012922_spleen | 0 .00 RPM | 5 .95 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_2445 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 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000011178 | 2 retrocopies |
retro_dnov_2445 , retro_dnov_851,
|
| Ictidomys tridecemlineatus | ENSSTOG00000011587 | 1 retrocopy |