RetrogeneDB ID: | retro_pabe_338 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 1:194118286..194119288(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAGT1 | ||
| Ensembl ID: | ENSPPYG00000020493 | ||
| Aliases: | None | ||
| Description: | magnesium transporter protein 1 precursor [Source:RefSeq peptide;Acc:NP_001124931] |
Retrocopy-Parental alignment summary:
>retro_pabe_338
GCAAATATGGCAGAAGTGTGGTGCCTTTGGCGTCTACTTTTGACCGTAGTGGTGGCCCTGTTATTCGTGGCTCCCGGGGT
TCCTACACATCCTTCCCGATGGAAGAAGGTGTTGGCCAAAAAGGTCAGCCAGCTGATGGATTGGACCAAGAAAGACAGAG
TGATAAGAATGAGTGACACCATGTTCTATCATTTTGTATTAGATGCACCAAAAAACTATTCTGTTATTGTGATGCTTACT
GCTCTCCACGAGTTCAGTTCATGTGTAATGTGCAAAGGTGCTGCTGAAGAATTTCAGATCTTGGCAAATTCCTATCAACG
CCCTGGTGCATTCACCACAAAGGTATTTTTTGCAATGGTGGATTATGATGAAAGCCCTGAGGTCTTTGAAGCGCTCCAGG
TAATGTCAGTTCCGAGTTTCTTCCACTTTTCTGCCCAATGGAAATTTACAACAGATGACATTTATAATTTGAGAGGAAGG
GATATTGTTGCTGACCAAATAGCTGAATGGGTAGCAGAAAGAACACATGTTAGCGTCAGAATCAGACAGCCTACAAATTA
TCATGGTCTCCTCAAGCCGGGGATACTTTTGGCTCTCATTGGTGGACTTGGGTATTTCTTGAAATGGAATAGGAAATCTA
TTTCTTGCAGAATTTTGTGCGAAGTTTTAACTCTGTGCTTTGTGATTGTGATGACGTCTGGTCAAATGTGGACTTATATA
AGAGGAGAACCGTATGTCCAAAGGGACCCTCACACAGGACATAAACATTATATCAGTAAATTTAGTCAGGCTCAGTTTGC
AGCAGAAACATTCATTATTTCCCTGTTTAATATGTGTGTTAGCCTGGGAATGGTGCTGTTAGACAAGGCTGCCACCTCTA
CGATGACCATCATAAAGAGAAAGATGATGTGTCTGGCTGGTATGTGTCTTGTTGCCATATTCTTCAGTTGGCTGCTTGCC
CTCTTTAGATTTAAAGTACCTGACTATCCATACAGCTTTGTC
ORF - retro_pabe_338 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.98 % |
| Parental protein coverage: | 91.28 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ANMAAGWWFWCVSVTVAVALLIVCD-VPSVSAQRKKEMVLSEKVSQLMEWTNKRPVIRMNGDKFRRLVKA |
| ANMA..W..W....TV.VALL.V...VP......KK..VL..KVSQLM.WT.K..VIRM....F...V.. | |
| Retrocopy | ANMAEVWCLWRLLLTVVVALLFVAPGVPTHPSRWKK--VLAKKVSQLMDWTKKDRVIRMSDTMFYHFVLD |
| Parental | PPRNYSVIVMFTALQLHRQCVVCKQADEEFQILANSWRYSSAFTNRIFFAMVDFDEGSDVFQMLNMNSAP |
| .P.NYSVIVM.TAL.....CV.CK.A.EEFQILANS.....AFT...FFAMVD.DE...VF..L...S.P | |
| Retrocopy | APKNYSVIVMLTALHEFSSCVMCKGAAEEFQILANSYQRPGAFTTKVFFAMVDYDESPEVFEALQVMSVP |
| Parental | TFINFPAKGKPKRGDTYELQVRGFSAEQIARWIADRTDVNIRVIRPPNYAGPLMLGLLLAVIGGLVYLRR |
| .F..F.A..K....D.Y.L..R...A.QIA.W.A.RT.V..R...P.NY.G.L..G.LLA.IGGL.Y... | |
| Retrocopy | SFFHFSAQWKFTTDDIYNLRGRDIVADQIAEWVAERTHVSVRIRQPTNYHGLLKPGILLALIGGLGYFLK |
| Parental | SNMEFLFNKTGWAFAALCFVLAMTSGQMWNHIRGPPYAHKNPHTGHVNYIHGSSQAQFVAETHIVLLFNG |
| .N..............LCFV..MTSGQMW..IRG.PY....PHTGH..YI...SQAQF.AET.I..LFN. | |
| Retrocopy | WNRKSISCRILCEVLTLCFVIVMTSGQMWTYIRGEPYVQRDPHTGHKHYISKFSQAQFAAETFIISLFNM |
| Parental | GVTLGMVLLCEAATSDMDIGKRKIMCVAGIGLVVLFFSWMLSIFRSKYHGYPYSFL |
| .V.LGMVLL..AATS.M.I.KRK.MC.AG..LV..FFSW.L..FR.K...YPYSF. | |
| Retrocopy | CVSLGMVLLDKAATSTMTIIKRKMMCLAGMCLVAIFFSWLLALFRFKVPDYPYSFV |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .22 RPM | 5 .20 RPM |
| SRP007412_cerebellum | 0 .61 RPM | 7 .05 RPM |
| SRP007412_heart | 0 .00 RPM | 17 .31 RPM |
| SRP007412_kidney | 1 .23 RPM | 24 .73 RPM |
| SRP007412_liver | 0 .06 RPM | 28 .49 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_338 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_338 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_338 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Gorilla gorilla | retro_ggor_377 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Gorilla gorilla | ENSGGOG00000010342 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000012886 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000000203 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000020493 | 1 retrocopy |
retro_pabe_338 ,
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