RetrogeneDB ID: | retro_dnov_2085 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_465:103258..103958(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LIX1 | ||
| Ensembl ID: | ENSDNOG00000012335 | ||
| Aliases: | None | ||
| Description: | Lix1 homolog (chicken) [Source:HGNC Symbol;Acc:18581] |
Retrocopy-Parental alignment summary:
>retro_dnov_2085
GTGAGTGTGGTGGAGGCGCTGCAGCAGTTCTGGCAGATGAAGCAGTCCCTTGGGGCTGACTTGAAGAATGGGGCTTTAGC
GGTTTTGAGATGGTGCCTACCAACAGCCCTCTCTATGTCTGCTATGTCACCCTGCCGGGGGGAAGTTGCTTTGGGAGTTT
CCAGGTTTGTCCCACAAAAGCTGAGGCTCGGCGGAGTGCTGCAAAGATTGCACTAATGAACTCTGTGTTTAATGCACATC
CTTCCCGGAGAATCACTGATGAGTTCATTGAGAAGAGTGTCTCTGAGCCTTTGGCATCTTTCAGCGGCAACAGGGAGGAG
GCTGACAACCCAAATACAGGGACTGGTGCCTTCGGATTCATGTTGGAACCCAACAAGGGCAAGTCAGTGTTGGAGTTCCA
GGAGTTAATGACAGTTTTTCAACTGCTGCACTGGAATGGCAGCCTTCAGGCCATGAGGGAAAGACCGAGCTCTCAGCAAG
AGGTGCTGGCTCATTATTCACCCCCAGCCCTGGATGATGATATTCGCCACCAAATGGCATTGCACTGGGTGAGCCGGGAG
AGAGTGTGCCAGGGGCACTGTCTAGAGAGCTGGCCTCCACTGAGTGGGAGCTGGATGAAGCCTGGCTGGGAGGCAAGTTG
CTGTGCTTCCACAAGGAGAAGAAAGATATTCTCATGCTGGCTGCTGGGCAGTTGGGCAAC
ORF - retro_dnov_2085 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.27 % |
| Parental protein coverage: | 82.92 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LNVVSMLQEFWESKQQQRAAFPSEGIVV-YESLPSPGPPFVSYVTLPGGSCFGNFQCCLSRAEARRDAAK |
| ..VV..LQ.FW..KQ...A........V..E..P...P..V.YVTLPGGSCFG.FQ.C...AEARR.AAK | |
| Retrocopy | VSVVEALQQFWQMKQSLGADLKNGALAV<FEMVPTNSPLYVCYVTLPGGSCFGSFQVCPTKAEARRSAAK |
| Parental | VALINSLFNELPSRRITKEFIMESVQEAVASTSGTLDDADDPSTSIGAYHYMLESNMGKTMLEFQELMTI |
| .AL.NS.FN..PSRRIT.EFI..SV.E..AS.SG....AD.P.T..GA...MLE.N.GK..LEFQELMT. | |
| Retrocopy | IALMNSVFNAHPSRRITDEFIEKSVSEPLASFSGNREEADNPNTGTGAFGFMLEPNKGKSVLEFQELMTV |
| Parental | FQLLHWNGSLKALRETKCSRQXXXXXXXXXXXXXXXXXXMALDWIMKR-ES-PGILSQELRMVLRELEEA |
| FQLLHWNGSL.A.RE...S.Q..................MAL.W.....ES.PG.LS.EL.....EL.EA | |
| Retrocopy | FQLLHWNGSLQAMRERPSSQQEVLAHYSPPALDDDIRHQMALHWVSRE<ESVPGALSRELASTEWELDEA |
| Parental | RKAGQELRFYKEKKEIVSLALTQIYN |
| ...G..L.F.KEKK.I..LA..Q..N | |
| Retrocopy | WLGGKLLCFHKEKKDILMLAAGQLGN |
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 .17 RPM | 0 .78 RPM |
| SRP012922_cerebellum | 1 .37 RPM | 1 .92 RPM |
| SRP012922_heart | 2 .09 RPM | 0 .00 RPM |
| SRP012922_kidney | 0 .82 RPM | 0 .00 RPM |
| SRP012922_liver | 2 .01 RPM | 0 .00 RPM |
| SRP012922_lung | 3 .82 RPM | 0 .00 RPM |
| SRP012922_quadricep_muscle | 0 .69 RPM | 0 .17 RPM |
| SRP012922_spleen | 4 .92 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_2085 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000012335 | 1 retrocopy |
retro_dnov_2085 ,
|
| Equus caballus | ENSECAG00000021643 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000047786 | 1 retrocopy |