Sequence
atgc intronic sequence ATGC exonic sequenceGTCCAAGAAAGACAACTTATACAAGGATGCAATGGAGACTTGCTCACAGTCTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAGgtaagaattctctatttgtgtctgcgggcaattgaagttgaaagaaacatctacactactgatgtctatgacaccctaagaaaattttataatttttttctgcgttgtaatttgtgatgtacag
Basic information
species | Physcomitrella patens |
transcript | PP1S147_10V6.1 |
intron # | 15 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 27
GTCCAAGAAAGACAACTTATACAAGGATGCAATGGAGACTTGCTCACAGTCTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAGgtaagaattctctatttgtgtctgcgggcaattgaagttgaaagaaacatctacactactgatgtctatgacaccctaagaaaattttataatttttttctgcgttgtaatttgtgatgtacag
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GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgtttgatttaagcccataaatttctatcttattt---ttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat---------------------
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
GTCCAAGAAAGACAACTTATACAAGGATGCAATGGAGACTTGCTCACAGTCTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAGgtaagaattc--tctatttgtgtctgcgggcaattgaagttgaaagaaacatctacactactgatgtctatgacaccctaagaaaattttataatttttttctgcgttgtaatttgtgatgtacag
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GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctatt-----ttgtttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat---------------------
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 26
GTCCAAGAAAGACAACTTATACAAGGATGCAATGGAGACTTGCTCACAGTCTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAGgtaagaattctctatttgtgtctgcgggcaattgaagttgaaagaaacatctacactactgatgtctatgacaccctaagaaaattttataatttttttctgcgttgtaatttgtgatgtacag
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GTCAAAGAAAGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtaccaaat-tcaattt-caacggcatataattcattttttagcaacattgcccagcattctcatttaacatgttttatttgaagactaagatgctaagcta----------------------
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 27
GTCCAAGAAAGACAACTTATACAAGGATGCAATGGAGACTTGCTCACAGTCTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAGgtaagaattctctatttgtgtctgcgggcaattgaagttgaaagaaacatctacac-tactgatgtctatgaca--ccctaagaaaattttataatttttttctgcgttgtaatttgtgatgtacag
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GTCAAAGAAAGACAACCTATACAAAGATGCGATGGAGACATGCTCTCAGTCTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtcatatacacttgtctataaa-agctgaaattgagataatcatcatcaaatgctaaatagtgtgaatgttccttcataaattttctaattttta--------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162186243|gb|FC362175.1|FC362175EST: CTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAG GGCAAAAAAGAGTGCTTCGCTGCTTGTCTATACACTTGTTACGACCTTATC
genomic: CTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAGgtaagaattc ... tgatgtacagGGCAAAAAAGAGTGCTTCGCTGCTTGTCTATACACTTGTTACGACCTTATC
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCCAAGAAAGACAACTTATACAAGGATGCAATGGAGACTTGCTCACAGTCTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAGgtaagaattctctatttgtgtctgcgggcaattgaagttgaaagaaacatctacactactgatgtctatgacaccctaagaaaattttataatttttttctgcgttgtaatttgtgatgtacag
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT