Sequence
atgc intronic sequence ATGC exonic sequence...ctcggtgtataatcacctgttaagctccgttcctgctcactgcttgactttcattaggcttgatcttagtgtattttattaatcctcatggaaaccgcagTCCCCAAGTGACTATTGCAACTGCCATTGTATTCTGCCATCGGTTTTTCCATCGACAATCACATGCAAAAAATGACAGACTT
Basic information
species | Physcomitrella patens |
transcript | PP1S119_132V6.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G308570_T02 (Zea mays), 3'ss of exon 10
ctcggtgtataatcacctgttaagctccgttcctgctcactgcttgactttcattaggcttgatcttagtgtattttat-taatcctcatggaaaccgcagTCCCCAAGTGACTATTGCAACTGCCATTGTATTCTGCCATCGGTTTTTCCATCGACAATCACATGCAAAAAATGACAGACTT
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gcctgcatgttactgcacgttttatgatgt-cttgtttgagttgaaatcttttatatatgcaatttttattcttctaatgccaactaactccataatgtagGCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGG
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 1
-ctcggtgtataatcacctgttaagctccgttcctgctcactgcttgactttcattaggcttgatcttagtgtattt-tattaatcctcatggaaaccgcagTCCCCAAGTGACTATTGCAACTGCCATTGTATTCTGCCATCGGTTTTTCCATCGACAATCACATGCAAAAAATGACAGACTT
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tgcctgcatgctactgcacgggttgtgatat-cttgtttgagttgaaaccttttttatatgtaatttttttcttctaatgctgatgaactttgtaat-gtagACCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTCTTTCTTCGTCAATCGCATGCCAAAAATGACAGACGG
upper sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 2
ctcggtgtataatcacctgttaagctccgttcctgctcactgcttgactttca-ttaggcttgatcttagtgtattttattaatcctcatggaaaccgcagTCCCCAAGTGACTATTGCAACTGCCATTGTATTCTGCCATCGGTTTTTCCATCGACAATCACATGCAAAAAATGACAGACTT
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atatttaatggatcctgcattcacaccaagtttgtcaaagtaaatacttttcgctcatccttttatctcgtaaaatctaccttacct-gtgctgtttttagGCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCTTCGTCAATCCCTTGCAAAAAATGATAGACGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactttcattaggcttgatcttagtgtattttattaatcctcatggaaaccgcagTCCCCAAGTGACTATTGCAACTGCCATTGTATTCTGCCATCGGTTTTTCCATCGACAATCACATGCAAAAAATGACAGACTT
tattaat putative branch site (score: 2)
atcttagtgtatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcggtgtataatcacctgttaagctccgttcctgctcactgcttgactttcattaggcttgatcttagtgtattttattaatcctcatggaaaccgcagTCCCCAAGTGACTATTGCAACTGCCATTGTATTCTGCCATCGGTTTTTCCATCGACAATCACATGCAAAAAATGACAGACTT
- - - - - - - - - - - - - - - - ctgctca