Sequence
atgc intronic sequence ATGC exonic sequence...gcgtcctgccttgtttagtttcttattctaagttttagttattccaattaattttcgtggtgccattttgttaataatctgtatggcttcttgtgcgcagGAAAAGTTTCTCGGAATTTGATCCGCGGTTAGTTGCCCCGACATGTCTGTACCTGGCCTCCAAAGCAGAAGAAAGCACAGTGCAGGCTAAGATTCTTGTT
Basic information
species | Physcomitrella patens |
transcript | PP1S18_263V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S18_263V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 5
gcgtcctgccttgtttagtttcttattctaagttttagttattccaattaattttcgt-----ggtgccattttgttaataatctgtatggcttcttgtgcgcagGAAAAGTTTCTCGGAATTTGATCCGCGGTTAGTTGCCCCGACATGTCTGTACCTGGCCTCCAAAGCAGAAGAAAGCACAGTGCAGGCTAAGATTCTTGTT
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ttatactatcttcgtctgaccctgaacgta-gtagtatatgc-ctaataaacttcccttaacaagtgtcaact-gatgactatcttcat--tttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
upper sequence: PP1S18_263V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 4
-gcgtcctgccttgtttagtttcttattctaagttttagt-tattcc-aattaattttcgtggtgccattttgttaataatc-tgtatggcttcttgtgcgcagGAAAAGTTTCTCGGAATTTGATCCGCGGTTAGTTGCCCCGACATGTCTGTACCTGGCCTCCAAAGCAGAAGAAAGCACAGTGCAGGCTAAGATTCTTGTT
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ataatactatcttcttctgaccctgg----aagttgtagtatatgcctaataaacttccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaattttcgtggtgccattttgttaataatctgtatggcttcttgtgcgcagGAAAAGTTTCTCGGAATTTGATCCGCGGTTAGTTGCCCCGACATGTCTGTACCTGGCCTCCAAAGCAGAAGAAAGCACAGTGCAGGCTAAGATTCTTGTT
tgttaat putative branch site (score: 3)
cttcttgt putative PPT
attttgttaataatct TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcgtcctgccttgtttagtttcttattctaagttttagttattccaattaattttcgtggtgccattttgttaataatctgtatggcttcttgtgcgcagGAAAAGTTTCTCGGAATTTGATCCGCGGTTAGTTGCCCCGACATGTCTGTACCTGGCCTCCAAAGCAGAAGAAAGCACAGTGCAGGCTAAGATTCTTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA