RetrogeneDB ID: | retro_pabe_3255 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 8:52095308..52095981(+) | ||
| Located in intron of: | ENSPPYG00000018580 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | F3 | ||
| Ensembl ID: | ENSPPYG00000001139 | ||
| Aliases: | None | ||
| Description: | tissue factor precursor [Source:RefSeq peptide;Acc:NP_001126163] |
Retrocopy-Parental alignment summary:
>retro_pabe_3255
CTGGCGACTCCAGCCTGGGCCTGGGTCCCACGTCCTGAGACTGCCTTAGCTCAGATTCTCCTGCTCCGCCAGGTCCTCCT
CAAGGCGGCTAGTGCTTCTGGCACTGCAGATAGAGTGGTAGCATATAATGTATAATCAACGAATTTCAAGACAATTTTGG
AGCTGGAACCCAAGCCTATCATCAATCATGTCTACACTGCCCAGACAAGCTCTGCATCAGGAGACTGGAAAAGCCATGCT
TGGAAACCCTGGACACAGAGAGTGACCTCACAGATTGGACAGCAAGGACGTGACACAGTCGTCCTCGGCCCAGGGCCCTT
CCTGCCCCGCTGGGGATGCAGCCACCAAGGGTTCTGCCGGGAACCTCTGATCCGAAGCTCCCCAGAGTTTACACGTGACC
TGGAGAAACACCTGGGACAGCCAGCAATTCAGTGTTTTGAATCAGTCAGGACAAAACAACGTGACAGTATCAGAATGACG
TACCTTAGAAAGAATGACATATTCCTAGGCCTCTGGGAGTTTGCGACAAGTACTCAAGTTGTACACTTTATTATTGGAAA
GCTTCATGTACGGGAAAGAAAACAGCCAAGACAAACACAAATGCGTTTTTGATAGATATGGATAAAGGGGAAACCACCGT
TCCAGTGTTCAGTGATTCCATCCGAAGACTACA
ORF - retro_pabe_3255 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.74 % |
| Parental protein coverage: | 77.63 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | METPAWPRVPRPETAVAWTLLLGWVFAQVAGASGTTNTVAAYNLTWKSTNFKTILEWEPKPL-NQVYTVQ |
| ..TPAW..VPRPETA.A..LLL..V....A.ASGT...V.AYN....STNFKTILE.EPKP..N.VYT.Q | |
| Retrocopy | LATPAWAWVPRPETALAQILLLRQVLLKAASASGTADRVVAYNV*--STNFKTILELEPKPIINHVYTAQ |
| Parental | ISTKTGDWKSK-CFYTADTECDLTDEIV-KDVKQTYLARVFSYPAGNVGSTGSAG-EPLYENSPEFTPYL |
| .S...GDWKS..C..T.DTE.DLTD....KDV.Q...A...S.PAG.....GSAG.EPL...SPEFT..L | |
| Retrocopy | TSSASGDWKSH<CLETLDTESDLTDWTA<KDVTQSSSAQGPSCPAGDAATKGSAG<EPLIRSSPEFTRDL |
| Parental | ETNLGQPTIQSFEQVGTKVNVTVQDERTLVRRNNTFLSLRD-VFGKDLIYTLYYWKSSSSGKKTAKTNTN |
| E..LGQP.IQ.FE.V.TK.........T..R.N..FL.L...V..K....TLYYWK.S..GKKTAKTNTN | |
| Retrocopy | EKHLGQPAIQCFESVRTKQRDSIR--MTYLRKNDIFLGLWE<VCDKYSSCTLYYWKASCTGKKTAKTNTN |
| Parental | EFLIDVDKGE-NYCFSVQAVIPSRT |
| .FLID.DKGE.N...SVQ...P..T | |
| Retrocopy | AFLIDMDKGE<NHRSSVQ*FHPKTT |
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 .00 RPM | 13 .99 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .80 RPM |
| SRP007412_heart | 0 .00 RPM | 11 .23 RPM |
| SRP007412_kidney | 0 .00 RPM | 10 .64 RPM |
| SRP007412_liver | 0 .00 RPM | 1 .81 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3255 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3255 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3255 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000117525 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000014683 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000011112 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000001139 | 2 retrocopies |
retro_pabe_3255 , retro_pabe_3256,
|