Sequence
atgc intronic sequence ATGC exonic sequencegtattgtttttgggtttctagtgctcatataataaagatagattcttatgcttatcactgtatgtttggtagctaagtgtaagaaggtaaatttgattttaatttgagggaaatattgcacatctataactgattttctgccctgtacatatgcagAGAAGTCTTATTCATATGCTCCCAAATTTCAACGAATGCTGGTGGGATAGCTTTGTCCTAGACGTATTAATTTGCAATTGGTTTG
Basic information
species | Physcomitrella patens |
transcript | PP1S159_14V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S159_14V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 7
gtattgtttttgggtttctagtgctcatataataaagatagattcttatgcttatcactgtatgtttggtagctaagtgtaagaaggtaaatttgattttaatttgagggaaatattgcacatctataactgattttctgccctgtacata-tgcagAGAAGTCTTATTCATATGCTCCCAAATTTCAACGAATGCTGGTGGGATAGCTTTGTCCTAGACGTATTAATTTGCAATTGGTTTG
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-----------------------------------------------------------gtatgcat------ttaatcttacacgatcaatttatttttggcttctg-----tcttctgaatctagattccttacatagtttcacatgtcctgcagCTCACCTTTCGCCATATGCTGCCAAACTTTAATGAGTGTTGGTGGGATAGCATCGTACTAGACATATTAATCTGCAATTGGTTTG
upper sequence: PP1S159_14V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G095757_T02 (Zea mays), 3'ss of exon 7
gtattgtttttgggtttctagtgctcatataataaagatagattcttatgcttatcactgtatgtttggtagctaagtgtaagaaggtaaatttgattttaatttgagggaaatattgcacatctataactgattttctgccctgtacatatgcagAGAAGTCTTATTCATATGCTCCCAAATTTCAACGAATGCTGGTGGGATAGCTTTGTCCTAGACGTATTAATTTGCAATTGGTTTG
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-----------------------------------------------------------gtatactctttttgttgtggtcaaattcctgacttgtgctt---tccagactcaggttcctaatgtagagttg--tatgtgc----------tgcagCTCACTTTTCGTCATATGTTGCCAAATTTCAATGAGTGCTGGTGGGATAGCATTGTCCTAGACATATTGATATGCAATTGGTTTG
upper sequence: PP1S159_14V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 7
gtattgtttttgggtttctagtgctcatataataaagatagattcttatgcttatcactgtatgtttggta-gctaagtgtaagaaggtaaatttgattttaatttgagggaaatattgcacatcta--taactgattttctgccctgtacatatgcagAGAAGTCTTATTCATATGCTCCCAAATTTCAACGAATGCTGGTGGGATAGCTTTGTCCTAGACGTATTAATTTGCAATTGGTTTG
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--------------------------------------------------------------------gtatactctttatgttgtggtcaaataactcttgacttgtg-----ctttccaaacccaggttcctaatgtagtgttacatgtat-tgcagCTCACTTTTCGCCATATGTTGCCAAATTTCAACGAGTGCTGGTGGGACAGCATTGTCCTAGACATATTGATCTGCAATTGGTTTGMapped 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|162276276|gb|FC452409.1|FC452409EST: GAAATCAGCCGTTTCTATGGGCGCTCTCTATTGCTTTCGAGTTTTGTGAG AGAAGTCTTATTCATATGCTCCCAAATTTCAACGAATGCTGGTGGGATAGC
genomic: GAAATCAGCCGTTTCTATGGGCGCTCTCTATTGCTTTCGAGTTTTGTGAGgtattgtttt ... acatatgcagAGAAGTCTTATTCATATGCTCCCAAATTTCAACGAATGCTGGTGGGATAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgagggaaatattgcacatctataactgattttctgccctgtacatatgcagAGAAGTCTTATTCATATGCTCCCAAATTTCAACGAATGCTGGTGGGATAGCTTTGTCCTAGACGTATTAATTTGCAATTGGTTTG
aactgat putative branch site (score: 3)
aaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtttttgggtttctagtgctcatataataaagatagattcttatgcttatcactgtatgtttggtagctaagtgtaagaaggtaaatttgattttaatttgagggaaatattgcacatctataactgattttctgccctgtacatatgcagAGAAGTCTTATTCATATGCTCCCAAATTTCAACGAATGCTGGTGGGATAGCTTTGTCCTAGACGTATTAATTTGCAATTGGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG