RetrogeneDB ID: | retro_sscr_250 | ||
Retrocopylocation | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 10:75670003..75670531(-) | ||
| Located in intron of: | ENSSSCG00000011162 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | ZDHHC12 | ||
| Ensembl ID: | ENSSSCG00000005658 | ||
| Aliases: | None | ||
| Description: | zinc finger, DHHC-type containing 12 [Source:HGNC Symbol;Acc:19159] |
Retrocopy-Parental alignment summary:
>retro_sscr_250
GAGGAGGCCAAGGAAGAGCAGACAGCCATGGCTCCTCAGGCCATCCCTCTTCGGCGCTGCAGATTCTGCATGGTGCTGCA
ACCCTTGCGGGCCTGGCACTGCCATGAGTGCCGGCGTTGTGTCCACCGCTATGACCACCACTGCCCCTGGATGGAGAACT
GCATGGGGGAGCACAACCACCCTCTCTTCGTGGCCCACCTGGCACTGCAGCTGGTGGTGTTTCTGTGGGGCTTGTACCTG
GCATGGTCTGGCCTCCACTTCTTCCAGCCCTGGGGGCTCTGGCTGCAATTCAGCTGGCTCCTGTTGGCCACCTTCCTGCT
GCTGTCCCTCTTCCCCCTCGTGGCCGGCCTGCTCTTGGCCTCACACCTCTACCTGGTGGCCAGTAACACCACCACCTGGG
CGTTCATCTCTTCCCACCGCATCACCCATCTCCGCTAGCGCCCCGGCAACCCCTTCGACTGTGGCCTGGCCCGCAACCTG
GCCCACTTCTTCTGTGGATGGCCCTCGGGGTCCTGGGAGACCCTGTGG
GAGGAGGCCAAGGAAGAGCAGACAGCCATGGCTCCTCAGGCCATCCCTCTTCGGCGCTGCAGATTCTGCATGGTGCTGCA
ACCCTTGCGGGCCTGGCACTGCCATGAGTGCCGGCGTTGTGTCCACCGCTATGACCACCACTGCCCCTGGATGGAGAACT
GCATGGGGGAGCACAACCACCCTCTCTTCGTGGCCCACCTGGCACTGCAGCTGGTGGTGTTTCTGTGGGGCTTGTACCTG
GCATGGTCTGGCCTCCACTTCTTCCAGCCCTGGGGGCTCTGGCTGCAATTCAGCTGGCTCCTGTTGGCCACCTTCCTGCT
GCTGTCCCTCTTCCCCCTCGTGGCCGGCCTGCTCTTGGCCTCACACCTCTACCTGGTGGCCAGTAACACCACCACCTGGG
CGTTCATCTCTTCCCACCGCATCACCCATCTCCGCTAGCGCCCCGGCAACCCCTTCGACTGTGGCCTGGCCCGCAACCTG
GCCCACTTCTTCTGTGGATGGCCCTCGGGGTCCTGGGAGACCCTGTGG
ORF - retro_sscr_250 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.2 % |
| Parental protein coverage: | 73.95 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EEAKEEQTAMVPQAIPLRRCRFCMVLQPLRARHCRECRRCVRRYDHHCPWMENCVGERNHPLFVAYLALQ |
| EEAKEEQTAM.PQAIPLRRCRFCMVLQPLRA.HC.ECRRCV.RYDHHCPWMENC.GE.NHPLFVA.LALQ | |
| Retrocopy | EEAKEEQTAMAPQAIPLRRCRFCMVLQPLRAWHCHECRRCVHRYDHHCPWMENCMGEHNHPLFVAHLALQ |
| Parental | LVVLLWGLYLAWSGLRFFQPWGLWLRSSGLLLATFLLLSLFSLVAGLLLASHLYLVASNTTTWEFISSHR |
| LVV.LWGLYLAWSGL.FFQPWGLWL..S.LLLATFLLLSLF.LVAGLLLASHLYLVASNTTTW.FISSHR | |
| Retrocopy | LVVFLWGLYLAWSGLHFFQPWGLWLQFSWLLLATFLLLSLFPLVAGLLLASHLYLVASNTTTWAFISSHR |
| Parental | IAYLRQRPGNPFDRGLTRNLAHFFCGWPSGSWETLW |
| I..LR.RPGNPFD.GL.RNLAHFFCGWPSGSWETLW | |
| Retrocopy | ITHLR*RPGNPFDCGLARNLAHFFCGWPSGSWETLW |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 0 .00 RPM |
| SRP014902_testis | 0 .28 RPM | 0 .00 RPM |
| SRP018288_heart | 0 .00 RPM | 0 .00 RPM |
| SRP018288_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP018288_liver | 0 .00 RPM | 0 .00 RPM |
| SRP018288_lung | 0 .10 RPM | 0 .00 RPM |
| SRP018856_adipose | 0 .40 RPM | 0 .00 RPM |
| SRP035408_brain | 0 .19 RPM | 0 .00 RPM |
| SRP035408_liver | 0 .00 RPM | 0 .00 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_250 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_250 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_250 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000002667 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000005658 | 1 retrocopy |
retro_sscr_250 ,
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