Sequence
atgc intronic sequence ATGC exonic sequencegtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT
Basic information
species | Physcomitrella patens |
transcript | PP1S22_429V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgc--agGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT
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---------------------------------------------------------------------------------------------------------------gtaacaaaataagcagg-acttgctctcatttttaaaat-----gaatattgtcttgttatattcattgattactttttatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT
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---------------------------------------------------------------------------------------------------------------------gtatctccttcaagctgcttttgtttgatatatcttt-gtttattatcgt-tcatgtttgttgaaatctgatt-ctttttcagGTGGAGCATGTGAAAGCAGAGAGAAATTTACTTGCAGAGGTTGACAGCAATTGCATTGTGAAGCTGTATTGTTCTTTTCAAGATGAAGAGTATTTGTATC
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccatttta-atcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT
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-------------------------------------------------------------------------------------------------------------------------gtatttaaattccttcaagtggctttcgtttgacat---ttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT--------------
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-------------------------------------------------------------------------------------------------------------------------------------------gttattagactct--tgccaatcactccg--gtgctgatgctctcgtga---ttttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ16108 (Selaginella moellendorffii), 3'ss of exon 3
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT
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--------------------------------------------------------------------------------------------------------------------------gtatgatctttgcttt--ttaccaacatattcaagtg-----cttacgattttaat---------------attccagGTCGAGCATGTGAAGGCAGAGAGAAATCTCCTCGCTGAAGTCGACAGTAACTACATAGTTAAGCTGTACTGTTCTTTCCAAGACGACGAATACCTTTATCMapped 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|162170612|gb|FC347108.1|FC347108EST: TGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG GTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAAC
genomic: TGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacg ... actattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatctgaaggggattactttaccattttaatcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT
ttttaat putative branch site (score: 3)
tttaccattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT