RetrogeneDB ID: | retro_pabe_3201 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 7_random:9904204..9905341(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FSCN1 | ||
| Ensembl ID: | ENSPPYG00000017337 | ||
| Aliases: | None | ||
| Description: | fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus) [Source:HGNC Symbol;Acc:11148] |
Retrocopy-Parental alignment summary:
>retro_pabe_3201
CTCCCGTCCACCGCCACCATGACCGCCAACGGCACAGCCGAGGCAGTGCAGATCCAGTTCGGCCTCATCAACTGCCGCAA
CAAGTACCTGACGGCCGAGGCATTCGGGTTCAAGGTTAACGCGTTGGCCAGCAGCCTGAAGAAGCAGCAGATCTGGACGC
CGGAGCAGCCCCCTGACGAGGCGGGCAGCGCGGCCGTGTGCCTGCGCAGCCACCTGGGCCGCTACCTGGCGGCGGACAAG
GACGGCAACGTGACCTGCGAGCGCGAGGTGCCCGGTCCCGACTGCTGCTTCCTCATCGTGGCGCACGACGACGGCCGCTG
GTCGCTGCAGTCCGAGGAGCACCGGCGCTACTTCGGAGGCACCGAGGACCGCCTGTCGTGCTTCGCGCAGACGGTGTCCC
CCGCCGAGAAGCGGAGCGTGCACATCGCCATGCACCCTCAGGTCAACATCTACAGCGTCACCCGTAGGCGCTAGGCGCAC
CTGAGCGCGCGGCCGGCCGACGAGATCGCCGTGGACCGCGACGTGCCCTGGGGCATCGACTCGCTCATCATCCTCGCCTT
CCAGGACCAGCGCTACAGCGTGCAGACCGCCGACCACCGCTTCCTGCGCCATGACGGGCGCATGGTGGCGAGCCCGGAGC
CGGCCACTGGCTACACGCTGGAGTTCCGCTTCGGCAAGGTGGCCTTCGGCGGCTGCGAGGGTCCTTACCTGGCGCCGTGG
GAGCCCAGCAGCACGCTCAAGGCCGGCAAGGCCACCAAGGTGGGCAAGGACGAGCTCTTTGCCCTGGAGCAGAGCTGCGC
CCAGGTCGTGCTGCAGGCGGCCAACGAGAGGAATGTGTCCACGCGCCAGGGTATGGACCTGTCTGCCAATCAGGACGAGG
AGACCGACCAGGAGACCTTCCAGCTGGAGATCGACCGCGACACCAAAAAGTGTGCCTTCCGTACCCACACGGGCAAGTAC
TGGACGCTGACGGCCACTGGGGGCGTGCAGTCCACCGCCTCCACCCAGAATGCCAGCTGCTACTTCGACATTGAGCGGCG
TGACCGGCGCATCACACTGAGGGCGTCCAATGGCAAGTTTGTGACATCTAAGAAGAATGGGCAGCTGGCCGCCTCGGTGG
AGACAGCAGGGGACTCA
ORF - retro_pabe_3201 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.93 % |
| Parental protein coverage: | 85.36 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LSSTATMTANGTAEAVQIQFGLINCGNKYLTAEAFGFKVNASASSLKKKQIWTLEQPPDEAGSAAVCLRS |
| L.STATMTANGTAEAVQIQFGLINC.NKYLTAEAFGFKVNA.ASSLKK.QIWT.EQPPDEAGSAAVCLRS | |
| Retrocopy | LPSTATMTANGTAEAVQIQFGLINCRNKYLTAEAFGFKVNALASSLKKQQIWTPEQPPDEAGSAAVCLRS |
| Parental | HLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSEAHRRYFGGTEDRLSCFAQTVSPAEKWSV |
| HLGRYLAADKDGNVTCEREVPGPDC.FLIVAHDDGRWSLQSE.HRRYFGGTEDRLSCFAQTVSPAEK.SV | |
| Retrocopy | HLGRYLAADKDGNVTCEREVPGPDCCFLIVAHDDGRWSLQSEEHRRYFGGTEDRLSCFAQTVSPAEKRSV |
| Parental | HIAMHPQVNIYSVTRKRYAHLSARPADEIAVDRDVPWGVDSLITLAFQDQRYSVQTADHRFLRHDGRLVA |
| HIAMHPQVNIYSVTR.R.AHLSARPADEIAVDRDVPWG.DSLI.LAFQDQRYSVQTADHRFLRHDGR.VA | |
| Retrocopy | HIAMHPQVNIYSVTRRR*AHLSARPADEIAVDRDVPWGIDSLIILAFQDQRYSVQTADHRFLRHDGRMVA |
| Parental | RPEPATGYTLEFRSGKVAFRDCEGRYLAPSGPSGTLKAGKATKVGKDELFALEQSCAQVVLQAANERNVS |
| .PEPATGYTLEFR.GKVAF..CEG.YLAP..PS.TLKAGKATKVGKDELFALEQSCAQVVLQAANERNVS | |
| Retrocopy | SPEPATGYTLEFRFGKVAFGGCEGPYLAPWEPSSTLKAGKATKVGKDELFALEQSCAQVVLQAANERNVS |
| Parental | TRQGMDLSANQDEETDQETFQLEIDRDTKKCAFRTHTGKYWTLTATGGVQSTASTKNASCYFDIEWRDRR |
| TRQGMDLSANQDEETDQETFQLEIDRDTKKCAFRTHTGKYWTLTATGGVQSTAST.NASCYFDIE.RDRR | |
| Retrocopy | TRQGMDLSANQDEETDQETFQLEIDRDTKKCAFRTHTGKYWTLTATGGVQSTASTQNASCYFDIERRDRR |
| Parental | ITLRASNGKFVTSKKNGQLAASVETAGDS |
| ITLRASNGKFVTSKKNGQLAASVETAGDS | |
| Retrocopy | ITLRASNGKFVTSKKNGQLAASVETAGDS |
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 .06 RPM | 36 .22 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 5 .84 RPM |
| SRP007412_heart | 0 .09 RPM | 0 .90 RPM |
| SRP007412_kidney | 0 .03 RPM | 4 .94 RPM |
| SRP007412_liver | 0 .00 RPM | 7 .04 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3201 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3201 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3201 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000075618 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000001028 | 1 retrocopy | |
| Ornithorhynchus anatinus | ENSOANG00000030243 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017337 | 3 retrocopies |
retro_pabe_1225, retro_pabe_3201 , retro_pabe_3544,
|