RetrogeneDB ID: | retro_dnov_1505 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_220380:442..1452(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZSCAN4 | ||
| Ensembl ID: | ENSDNOG00000011483 | ||
| Aliases: | None | ||
| Description: | zinc finger and SCAN domain containing 4 [Source:HGNC Symbol;Acc:23709] |
Retrocopy-Parental alignment summary:
>retro_dnov_1505
ATGGCTTTAGATCTCAGAACTTCCTTTCGACAGGACCCATCCAGGAGTGATCATCCTGGGTCACACAATCTAGAGCTTGA
ACCTACCCAAGGACATGATCTCCAGAGGAGAGAGGGGAACTCTAAGTTCCAGGGCCCTCAGCTCAGCTTATATCAAACCA
GCAATGACTCATTTGCAAAGCAGGAACTAAAAAGACTGGAAGGTATTTCACTTGTGGCTGCAGCCAGAAAAACACAGCAA
GGAAGAAATTATTTCTCAATTGATACTGGAACAGCTTGTGAGGAATGGATACTGCAGGAACAGGTCCACTTTGAAAGAAA
AATGGGATTCAAGTGGAAGAAATCTGGAGAAACTCATGGGAGAGCTGAATGATGACTGCATGAAGTCACCTGATTTTGTC
CATGTCCACATGCAGGGACAGGAAGTCCTCTTCTCAGAGAATATGCCCTTAAGAGAAGTCATTTATCTCATGGAACAAAT
GTCAGCAGGAACCAAGAAGAGAGAGCATGAGGACACCCTTCCAAGGTCCCCAAAATATTCCCCTTCAAACAGGACATGGA
GATGAATATAAAGATGACAGTAACATTTTTGTGAAATGCAATCAAATCAATGTCAATATTACTAGTCAAGGAAATCAAGT
ACCTTCCATGGTTATTATTCAGGAGATGATAGCCCTAAGCCTGAGAGGGGAGTGGTTCCTGGGAGAACCTGCATAACTCC
AGAAGAGCAGAGCTTGGCTCCTCCATATCCCAGAAAGGATCCCTAGGATGATCTTCTCAAGATGTCCTTATGGAGGTGGA
ACCACAGTTTCTCCCCAGGATAGATCTAGCCATCTCTAAGCCTTTCCCTACCAACCAAAGCAATGATGGAATATACAGAT
GTGGAATAAACCAAGAAAGTGTCCACAGTTACCCAAAATCACATAAGTATGAGAACTGTCCCAGGATCCTTAGGTACCAG
CTCAGCTAGACACCCACCAGAGAAGACACAAGAATGTGAGATCATTTGTT
ORF - retro_dnov_1505 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.1 % |
| Parental protein coverage: | 78.52 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | MALDLRTSFRHDPSRSGHPGSHNLELEPTQGCDLQRREGNSKFQ-GPQLSLYQTSNGSFAKQELKRLR-K |
| MALDLRTSFR.DPSRS.HPGSHNLELEPTQG.DLQRREGNSKFQ.GP...L.........K...K....K | |
| Retrocopy | MALDLRTSFRQDPSRSDHPGSHNLELEPTQGHDLQRREGNSKFQ<GPSAQLISNQQ*LICKAGTKKTG<K |
| Parental | VFHLWLQPEKHSKEEIISQLILEQLVMNGYCRNRSILKEKWDSSGRNLEKLVGELNDDCMKSPDFVHVHM |
| VFHLWLQPEKHSKEEIISQLILEQLV.NGYCRNRS.LKEKWDSSGRNLEKL.GELNDDCMKSPDFVHVHM | |
| Retrocopy | VFHLWLQPEKHSKEEIISQLILEQLVRNGYCRNRSTLKEKWDSSGRNLEKLMGELNDDCMKSPDFVHVHM |
| Parental | QGQEALFSENMPLREVIYLMEQMPAGTPRGESMRT-PFQGP-QNIPLQTGHGDEYKDDSNIFVKRNQINV |
| QGQE.LFSENMPLREVIYLMEQM.AGT...E...T.P...P.QNIPLQTGHGDEYKDDSNIFVK.NQINV | |
| Retrocopy | QGQEVLFSENMPLREVIYLMEQMSAGTKKREHEDT<PSKVP<QNIPLQTGHGDEYKDDSNIFVKCNQINV |
| Parental | NITSQGNQVPYVVIIQE-DDSPKPE-EGSGSWKNLHNFRRAELGSPTSQEGSLGESSSQDVPMEVETQFL |
| NITSQGNQVP..VIIQE.DDSPKPE.EGSGSW.NLHN.RRAELGS..SQ.GSLG..SSQDV.MEVE.QFL | |
| Retrocopy | NITSQGNQVPSMVIIQE<DDSPKPE<EGSGSWENLHNSRRAELGSSISQKGSLG-*SSQDVLMEVEPQFL |
| Parental | PRTDQASPKPALTNQSSDGTSRCGINQERVHSPPKSYKCEDCPRIFRF-PSQLEAHQRRHRNERPFV |
| PR.D.A..KP..TNQS.DG..RCGINQE.VHS.PKS.K.E.CPRI.R..P.QL..HQRRH.N.R.FV | |
| Retrocopy | PRIDLAISKPFPTNQSNDGIYRCGINQESVHSYPKSHKYENCPRILRY<PAQLDTHQRRHKNVRSFV |
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 .19 RPM | 0 .00 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 0 .14 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .00 RPM |
| SRP012922_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP012922_liver | 0 .00 RPM | 0 .00 RPM |
| SRP012922_lung | 0 .00 RPM | 0 .00 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP012922_spleen | 0 .00 RPM | 0 .00 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_1505 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 16 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000005419 | 2 retrocopies | |
| Dasypus novemcinctus | ENSDNOG00000011483 | 11 retrocopies |
retro_dnov_1048, retro_dnov_1253, retro_dnov_1287, retro_dnov_1505 , retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556, retro_dnov_2666, retro_dnov_859, retro_dnov_964,
|
| Equus caballus | ENSECAG00000015200 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000003257 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000023779 | 1 retrocopy |