RetrogeneDB ID: | retro_dnov_340 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_3797:222727..223689(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GABPB2 | ||
| Ensembl ID: | ENSDNOG00000004312 | ||
| Aliases: | None | ||
| Description: | GA binding protein transcription factor, beta subunit 2 [Source:HGNC Symbol;Acc:28441] |
Retrocopy-Parental alignment summary:
>retro_dnov_340
AATGGTGCAGATGTGAATGCCAAAGACATGCTGAAGATGACAGCTTTGCATTGGGCCACAGAGCACCACCATCGAGATGC
TGTAGAGCTACTTATTAAGTATGGAGCTGATGTCCATGCTTTCAGCAAATTTGATAAATCTGCCTTTGACATAGCCCCTG
GAGAAGAACAATGCTGAGATTCTGGTCATCCTCCAGGAAGCAATGCAGAATCAGGTGAATGCTAATCCCGAGAGAACCAA
TCCTGTGACTAACTCTGTGAGTATGGCTGCTCCATTTATCTTCACATCTGGGAGAAGTTGTCAACCTTGCTAGCCTTGTT
TCTTCAGCCAACACCAAAACAACCTCAGGTGACCCCCATGCCTCAACAGTACAGTTCTCAAATTATACCACCTCAGTGCT
GGCCACCCTTGCAGCTCTTGCTGAGGCATCAGCCCCCCTCTCCAACTCACACAGAGCCACAGCCAATTCAGAGGAAATCA
TAGAGGGAAATTCTGTTGATCCCTCAGTCCAGCAAATGATGGGGAGTGGAGGCCAGAGAGTCATTACCATAGTGACTGAT
GGAGTCCCTCTGGGTAATCTTCAAACTGCAATCCCTACTGGAGGCATTGGCCAGCCATTTATTGTAACAATGCAAGATGG
ACAGCAAGTTCTAACTGTACCTGCTGGTCAGGTTGCAGAGGAGACCGTAATTGAAGAGGAGGAAGAAGACGAAGAAAAGT
TGCCACTGACTAAGAAACCAAGGATAGAAGAGATAATAAACAGTGTGGAGGAAAGGAAGGAAGGCAGTGAAAGAGAGCTG
CTACAGCAGCAGCTCCAGGAGGCCAATCGAAGAGCCCAGGAATACCGACACCAGCTTCTAAAGAAAGAGCAGGAGGCAGA
ACAGTACCGCCTCAAATTGGAAGCCATGGCCCGGCAACAACCCAATGGAGTTGATATTACCATGGTTGAAGAGGTGGCTG
AG
ORF - retro_dnov_340 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.45 % |
| Parental protein coverage: | 71.11 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | NGADVNAKDMLKMTALHWATEHHHRDVVELLIKYGADVHAFSKFDKSAFDIA-LEKNNAEILVILQEAMQ |
| NGADVNAKDMLKMTALHWATEHHHRD.VELLIKYGADVHAFSKFDKSAFDIA.LEKNNAEILVILQEAMQ | |
| Retrocopy | NGADVNAKDMLKMTALHWATEHHHRDAVELLIKYGADVHAFSKFDKSAFDIA>LEKNNAEILVILQEAMQ |
| Parental | NQVNANPERTNPVTNSVSMAAPFIFTSG-EVVNLASLVSSANTKTTSGDPHASTVQFSNYTTSVLATLAA |
| NQVNANPERTNPVTNSVSMAAPFIFTSG.EVVNLASLVSSANTKTTSGDPHASTVQFSNYTTSVLATLAA | |
| Retrocopy | NQVNANPERTNPVTNSVSMAAPFIFTSG>EVVNLASLVSSANTKTTSGDPHASTVQFSNYTTSVLATLAA |
| Parental | LAEASAPLSNSHRATANSEEIIEGNSVDPSIHQMMGSGGQRVITIVTDGVPLGNLQTAIPTGGIGQPFIV |
| LAEASAPLSNSHRATANSEEIIEGNSVDPS..QMMGSGGQRVITIVTDGVPLGNLQTAIPTGGIGQPFIV | |
| Retrocopy | LAEASAPLSNSHRATANSEEIIEGNSVDPSVQQMMGSGGQRVITIVTDGVPLGNLQTAIPTGGIGQPFIV |
| Parental | TMQDGQQVLTVPAGQVAEETVIEEEEEDEEKLPLTKKPRIEEIINSVEERKEGSERELLQQQLQEANRRA |
| TMQDGQQVLTVPAGQVAEETVIEEEEEDEEKLPLTKKPRIEEIINSVEERKEGSERELLQQQLQEANRRA | |
| Retrocopy | TMQDGQQVLTVPAGQVAEETVIEEEEEDEEKLPLTKKPRIEEIINSVEERKEGSERELLQQQLQEANRRA |
| Parental | QEYRHQLLKKEQEAEQYRLKLEAMARQQPNGVDITMVEEVAE |
| QEYRHQLLKKEQEAEQYRLKLEAMARQQPNGVDITMVEEVAE | |
| Retrocopy | QEYRHQLLKKEQEAEQYRLKLEAMARQQPNGVDITMVEEVAE |
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 | 6 .22 RPM |
| SRP012922_cerebellum | 0 .82 RPM | 5 .22 RPM |
| SRP012922_heart | 0 .00 RPM | 3 .25 RPM |
| SRP012922_kidney | 0 .55 RPM | 2 .19 RPM |
| SRP012922_liver | 0 .77 RPM | 2 .94 RPM |
| SRP012922_lung | 0 .92 RPM | 8 .86 RPM |
| SRP012922_quadricep_muscle | 0 .52 RPM | 1 .73 RPM |
| SRP012922_spleen | 2 .06 RPM | 12 .13 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_340 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 | ENSDNOG00000004312 | 1 retrocopy |
retro_dnov_340 ,
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