Sequence
atgc intronic sequence ATGC exonic sequencegtacgcacaactttctagttgccagtgagaaactggttgggactttgttgcctttttacaaatattagtgtaaaggattatgtattgagttcgaaggagctacgactcatttggaagagattttctaagtagagcttctcatggaacaaattacttaaacctgaagctttgttgaccgatgttctttttatagGATGGCTCATGCAATGGCTTACAACATTATGCAGCATTAGGTCGAGATCGA
Basic information
species | Physcomitrella patens |
transcript | PP1S246_118V6.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S246_118V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G115564_T02 (Zea mays), 3'ss of exon 9
gtacgcacaactttctagttgccagtgagaaactggttgggactttgttgcctttttacaaatattagtgtaaaggattatgtattgagttcgaaggagctacgactcatttggaagagattttctaagtagagcttctcatggaacaaattacttaaac-ctgaagctttgttgaccgatgttctttttat-agGATGGCTCATGCAATGGCTTACAACATTATGCAGCATTAGGTCGAGATCGA
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---------------------------------------------------------------------------------------tatgcctagaaagtgc-atttgtt-------gatgctctgagcaattctgcatagcctacatttcatttcactgctaatttgttggttatcattgtttttgttgtcagGATGGTTCATGCAATGGTTTACAACATTATGCCGCTCTTGGAAGGGACTAT
upper sequence: PP1S246_118V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G440258_T01 (Zea mays), 3'ss of exon 6
gtacgcacaactttctagttgccagtgagaaactggttgggactttgttgcctttttacaaatattagtgtaaaggattatgtattgagttcgaaggagctacgactcatttggaagagattttctaagtagagcttctcatggaacaaattacttaaac-ctgaagctttgttgaccgatgttctttttat-agGATGGCTCATGCAATGGCTTACAACATTATGCAGCATTAGGTCGAGATCGA
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---------------------------------------------------------------------------------------tatgcctagaaagtgc-atttgtt-------gatgctctgagcaaatctgcatagcctacatttcatttcactgctaatttgttggttatcattgtttttgttgtcagGATGGTTCATGCAATGGTTTACAACATTATGCCGCTCTTGGAAGGGACTAT
upper sequence: PP1S246_118V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G165454_T01 (Zea mays), 3'ss of exon 7
gtacgcacaactttctagttgccagtgagaaactggttgggactttgttgcctttttacaaatattagtgtaaaggattatgtattgagttcgaaggagctacgactcatttggaagagattttctaagtagagcttctcatggaacaaattacttaaac-ctgaagctttgttgaccgatgttctttttat-agGATGGCTCATGCAATGGCTTACAACATTATGCAGCATTAGGTCGAGATCGA
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-------------------------------------------------------------------------------------catatgcctagaaagtgc-atttgtt-------gatgctctgagcaa--ctgcatagcctacatttcatttcaatgctaatttgttggttatcattgtttttgttgtcagGATGGTTCATGCAATGGTTTACAACATTATGCCGCTCTTGGAAGGGACTAT
upper sequence: PP1S246_118V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA18G51160.1 (Glycine max), 3'ss of exon 9
gtacgcacaactttctagttgccagtgagaaactggttgggactttgttgcctttttacaaatattagtgtaaaggattatgtattgagttcgaaggagctacgactcatttggaagagattttctaagtagagcttctcatggaacaaattacttaaacctgaagctttgttgaccgatgttctttttatagGATGGCTCATGCAATGGCTTACAACATTATGCAGCATTAGGTCGAGATCGA
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-----------------------------------------------------------------------------------attgtcattgtcaatttta----tcattttccatctgtgtatggaatgaatccatgttt---attaactaatca---ctgaatctgtactaccataattttctctcctagGATGGCTCCTGTAATGGCTTACAACATTATGCTGCCTTGGGGAGAGACAAG
upper sequence: PP1S246_118V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 2
gtacgcacaactttctagttgccagtgagaaactggttgggactttgttgcctttttacaaatattagtgtaaaggattatgtattgagttcgaaggagctacgactcatttggaagagattttctaagtagagcttctcatggaacaaattacttaaacctgaagctttgttgaccgatgttctttttatagGATGGCTCATGCAATGGCTTACAACATTATGCAGCATTAGGTCGAGATCGA
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----------------------------------------------------------------------------atgttgca--aaactctaatatgggatcacttttcaatttaaacttttttctgtatg--ttttca------aaagtatttgttagtaatgctactctgatggaattt-------tagGATGGTTCCTGCAATGGCTTACAACACTATGCAGCTCTGGGAAGAGATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatggaacaaattacttaaacctgaagctttgttgaccgatgttctttttatagGATGGCTCATGCAATGGCTTACAACATTATGCAGCATTAGGTCGAGATCGA
tgttgac putative branch site (score: 3)
tgttcttttt putative PPT
aacaaattacttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcacaactttctagttgccagtgagaaactggttgggactttgttgcctttttacaaatattagtgtaaaggattatgtattgagttcgaaggagctacgactcatttggaagagattttctaagtagagcttctcatggaacaaattacttaaacctgaagctttgttgaccgatgttctttttatagGATGGCTCATGCAATGGCTTACAACATTATGCAGCATTAGGTCGAGATCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC