RetrogeneDB ID: | retro_dnov_521 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_5632:2450..3050(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000006702 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C8orf33 | ||
| Ensembl ID: | ENSDNOG00000015805 | ||
| Aliases: | None | ||
| Description: | chromosome 8 open reading frame 33 [Source:HGNC Symbol;Acc:26104] |
Retrocopy-Parental alignment summary:
>retro_dnov_521
ATGGCAGTCCCTGGACACCCTGCTCGGGAGACTTCGGCGGCCGCAGCCCCAGGTGCGGCCCGCGTGCCTCACACCGGCCC
CCTGGCCCGGCTCTCAGCGCCCCGACTCTTTCCTCTGTAACATCATCCAGCGCATCTCTGCCCCGGGCACCCACCTGTAA
TGACGCTGTCCCCAGGGTGCTCCCCGTAGGCGATGACGGTGATGCAGCCTCTAAGAAGCAAAAGAAGAATAAGAAGAAAA
CCGGGAACGGGGCGTCTGTGGCAAATGGAGGCGGGAAGGCCTCAGAAAAGCTGGCCCCAGAGGAGCCCTAAGTGCTGAGG
CCCAGGCAGAGCAGCTGGCCCAGGAACTGGCTTGGTGTGTGGAGCAGCTCCATCTGGATCTCAGGACCCAGAGACCCAGC
CCAAAACAGAAAGAGCAGGCTACTGGAGCAATCCGGACCCTCGTCAGCGAACCCCCCTGCCCCGGAAGAGGCAGCTCATG
CATTCCTTATTTGGGGACTACAGGACTCAGATGGAAGCAGAATGGAGAGGGGCCCTGCAGGCTCTCAGGGCTGCAGCCCA
TTCATCCCAGGTGAAGCCTGTAAGACCACCAGAAAGAAGA
ORF - retro_dnov_521 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.43 % |
| Parental protein coverage: | 87.12 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVSGHPARETAAAAAPGAARAPHAPRPPGPALSAPTLSSATSPPARLCPGRP-TCKDAVPRVLPAGDDG |
| MAV.GHPARET.AAAAPGAAR.PH....P...LSAP.L......PA.LCPG.P.TC.DAVPRVLP.GDDG | |
| Retrocopy | MAVPGHPARETSAAAAPGAARVPHTG--PLARLSAPRLFPL*HHPAHLCPGHP<TCNDAVPRVLPVGDDG |
| Parental | D-AASKKQKKKKKTRDGASVADGGGKASEKLVPEEP-LSAEAQAEQLAQELAWCVEQLQLGLRTQRPSPK |
| D.A.............GASVA.GGGKASEKL.PEEP.LSAEAQAEQLAQELAWCVEQL.L.LRTQRPSPK | |
| Retrocopy | DAASXXXXXXXXXXGNGASVANGGGKASEKLAPEEP<LSAEAQAEQLAQELAWCVEQLHLDLRTQRPSPK |
| Parental | QKEQATGAIRTLLSERTPLP-RKRQLMRSLFGDYRTQMEAERRETLQALRAAAHSSQVKPVSKAARK |
| QKEQATGAIRTL.SE..P.P.RKRQLM.SLFGDYRTQMEAE.R..LQALRAAAHSSQVKPV....R. | |
| Retrocopy | QKEQATGAIRTLVSE-PPCP<RKRQLMHSLFGDYRTQMEAEWRGALQALRAAAHSSQVKPVRPPERR |
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 | 12 .64 RPM |
| SRP012922_cerebellum | 0 .69 RPM | 6 .05 RPM |
| SRP012922_heart | 0 .00 RPM | 5 .10 RPM |
| SRP012922_kidney | 0 .27 RPM | 18 .34 RPM |
| SRP012922_liver | 0 .00 RPM | 4 .95 RPM |
| SRP012922_lung | 0 .00 RPM | 15 .27 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 6 .23 RPM |
| SRP012922_spleen | 0 .11 RPM | 13 .96 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_521 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 5 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000015805 | 3 retrocopies |
retro_dnov_1578, retro_dnov_406, retro_dnov_521 ,
|
| Macaca mulatta | ENSMMUG00000016084 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000028791 | 2 retrocopies | |
| Mustela putorius furo | ENSMPUG00000005972 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000034107 | 1 retrocopy |