Sequence
atgc intronic sequence ATGC exonic sequenceGTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatttcattataatatctcataacttttgcttcaaaataatcaaagactgtagtgacttagtacatatttctttttcacttggagcacc...
Basic information
species | Physcomitrella patens |
transcript | PP1S152_81V6.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 3
GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatt-tcattataatatctcataact-tttgcttcaaaataatcaaagactgtagtgacttagtacatatttctttttcacttggagcacc
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GTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAGgtacggttgttagttactactgtattgtaacttcagtgttctcatctgattatttgcccttttaaatacctccttgcttgtttctaccatgttatcaatt--
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT2G17130.2 (Arabidopsis thaliana), 5'ss of exon 3
GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatttcattataatatctcataacttttgcttcaaaataatcaaagactgtagtgacttagtacatatttctttttcacttggagcacc
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GTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAGgtaa--taataaaattcattttaccttgatctaa----tgtacaagcactatagagaagtagattctcttgct-tatgctatgaaattttctgtag----
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 3
GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatttcatt-ataatatctcataacttttgcttcaaaataatcaaagactgtagtgacttagtacatatttctttttcacttggagcacc-
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GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaacatcctgtattgatattctctcgagctatacattagtggataaagaatagttctaa--aatttatacatctgcgacattaaatacaaaaacag
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 3
GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatttcattataatatctcataacttttgcttcaaaataatcaaagactgtagtgacttagtacatatttcttt---ttcacttggagcacc
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GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAGgtaccttttctttttgaataatgaaaaacgaaaa--taaattagtagtgaagaagagattagaaaaatgaaggataaggaaccatgggttacctttcagcag-
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatttcattataatatctc-------ataacttttgcttcaaaataatcaaagactgta-gtgacttagtacatatttctttttcacttggagcacc
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GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatact-cacaatttcaagtttatatttcttcctccattattttttcttttcttctagaatatcatccacgcatcttaggacataaagtcaatgaacccg-------Mapped 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|162191774|gb|FC367507.1|FC367507EST: GGCCAATACTGCAGCTGGTATTGCANGCGGGACTGGAGTCATGCCTGGAG GCAACGTGGGTG
genomic: GGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctact ... ttgcctgcagGCAACGTGGGTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatttcattataatatctcataacttttgcttcaaaataatcaaagactgtagtgacttagtacatatttctttttcacttggagcacc
- - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaataa