RetrogeneDB ID: | retro_dnov_1221 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_16552:16193..17189(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000018047 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FOXM1 | ||
| Ensembl ID: | ENSDNOG00000006678 | ||
| Aliases: | None | ||
| Description: | forkhead box M1 [Source:HGNC Symbol;Acc:3818] |
Retrocopy-Parental alignment summary:
>retro_dnov_1221
ATGAAAACCAGCCCCCGTCGGCCACTGATTCTCAAAAGACGGAGACTGCCCCTTCATGTTCAAAATGCCCCAGGTGACAC
ATCAGAGGAAGAACCCAAGAGGCCCCCTGCCCAGGAAGAGCCTAGTCAAACGCAGGCCTCTAAGGAGGTGGCGGAACCCA
ACTCTTGCAAGTTTCCTGCAGGGATCAAGATTATTAACCATCCCACCATGCCCAACACCCAAGTGGTAGCCATCCCCAAC
AATGCCAACATCCAGAGCATCATTACAGCATTGACTGCCAAAGGAAAAGAAAGCGGCAGCAGTGGGCCCAACAAATTCAT
CCTCATCAGCTGTGGGGGAACCACCCCTCACCCACCGGGATCCCAGCCTCCAGCCCAAACCAGCAATGATGCCAAGACAG
AAGCGATAACTGAGACCCTGGGTCCAAAGCCTGCAGCGAGGGACACGAATCCTCCTAGACCGCCTGCAGCCCCTCCTGGG
CAGAGATGGGAGAGCTATGCTGCTGGTGAGGCTGTAGGCTGCGCGCTCGACAACAGCTTGACCAACATCCAGTGGCTTGG
AAAGATGAGTTCGGATGGACTGGACTCCTGCAGCATCAAACAAGAAATGGAGGACAAGGAGAATCGTCGCCTGGAGCAGA
GTCAGGTTAAGGTTGAGGAGCCCCCGGGAGCCTCAACATCCTGGCAGGACTCTGTGTCAGAGCGGCCACCCTACTCTTAC
ATGGCCATGATACAATTCGCCATCAACAGCACCGAGAAGAAGCACATGACCTTGAAAGACATCTACACCTGGATCGAGGA
CCACTTTCCCTATTTTAAGCATATCGCCAAGCCCGGCTGGAAGAATTCCATTCGCCACAACCTTTCTCTCCATGACATGT
TTGTTCGGGAGACGTCTGCCAATGGCAAGGTCTCCTTTTGGACCATTCACCCCAGCGCCAATCACTACTTGACGTTGGAC
CAGGTGTTCAAGCAGCAGAAACGACCCACTCCTGAG
ORF - retro_dnov_1221 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.88 % |
| Parental protein coverage: | 57.64 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MKTSPRRPLILKRRRLPLHVQNAPGDTSEEEPKRPPAQEEPSQTQASKEVAESNSCKFPAGIKIINHPTM |
| MKTSPRRPLILKRRRLPLHVQNAPGDTSEEEPKRPPAQEEPSQTQASKEVAE.NSCKFPAGIKIINHPTM | |
| Retrocopy | MKTSPRRPLILKRRRLPLHVQNAPGDTSEEEPKRPPAQEEPSQTQASKEVAEPNSCKFPAGIKIINHPTM |
| Parental | PNTQVVAIPNNADIQSIITALTAKGKESGSSGPNKFILISCGGATPHPPGSQPPAQTSTDAKTEVITETL |
| PNTQVVAIPNNA.IQSIITALTAKGKESGSSGPNKFILISCGG.TPHPPGSQPPAQTS.DAKTE.ITETL | |
| Retrocopy | PNTQVVAIPNNANIQSIITALTAKGKESGSSGPNKFILISCGGTTPHPPGSQPPAQTSNDAKTEAITETL |
| Parental | GPKSAARDTNPPRPPAAPPGQRWESYAAGEAVGCALDNSLTNIQWLGKMSSDGLDSCSIKQEMEDKENRR |
| GPK.AARDTNPPRPPAAPPGQRWESYAAGEAVGCALDNSLTNIQWLGKMSSDGLDSCSIKQEMEDKENRR | |
| Retrocopy | GPKPAARDTNPPRPPAAPPGQRWESYAAGEAVGCALDNSLTNIQWLGKMSSDGLDSCSIKQEMEDKENRR |
| Parental | LEQSQVKXXEPPGASTSWQDSVSERPPYSYMAMIQFAINSTEKKRMTLKDIYTWIEDHFPYFKHIAKPGW |
| LEQSQVK..EPPGASTSWQDSVSERPPYSYMAMIQFAINSTEKK.MTLKDIYTWIEDHFPYFKHIAKPGW | |
| Retrocopy | LEQSQVKVEEPPGASTSWQDSVSERPPYSYMAMIQFAINSTEKKHMTLKDIYTWIEDHFPYFKHIAKPGW |
| Parental | KNSIRHNLSLHDMFVRETSANGKVSFWTIHPSANRYLTLDQVFKPMDPGSPQ |
| KNSIRHNLSLHDMFVRETSANGKVSFWTIHPSAN.YLTLDQVFK......P. | |
| Retrocopy | KNSIRHNLSLHDMFVRETSANGKVSFWTIHPSANHYLTLDQVFKQQKRPTPE |
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 | 1 .36 RPM | 4 .86 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 0 .27 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .23 RPM |
| SRP012922_kidney | 0 .27 RPM | 0 .00 RPM |
| SRP012922_liver | 0 .00 RPM | 0 .00 RPM |
| SRP012922_lung | 0 .15 RPM | 0 .00 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP012922_spleen | 2 .98 RPM | 4 .69 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_1221 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000006678 | 1 retrocopy |
retro_dnov_1221 ,
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