Sequence
atgc intronic sequence ATGC exonic sequenceAAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgtattaacatttggacttttgtttcgaaagaaaagacgtatagttatcgtttgagttcgcagcatgttgtgtactaagtttctggcattcttgtcatgac...
Basic information
species | Physcomitrella patens |
transcript | PP1S357_34V6.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S357_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 9
AAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgtat-taacatttggacttttgtttcgaaagaaaagacgtatagttatcgtttgagttcgcagcatgttgtgtactaagtttctggcattcttgtcatgac--
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TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcctgccaactgtgctatacttttacatagtgttcagttatagat---gttctatttctttagttttatcaaatttcataaatcgcataaaagttg
upper sequence: PP1S357_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G020721_T01 (Zea mays), 5'ss of exon 9
-AAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgtatt------aacatttggacttt--------tgtttcgaaagaaaagacgtatagttatcgtttgagttcgcagcatg-ttgtgt-actaagtttctggcattcttgtcatgac-----------------------
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TAAACCAGATC-TTCCCCGGTTGCATGAATGGCAATTTCGATCTGGACTGGATCGCTACATTTGGATCGTGGGGATGATATATGCATATTACCATCCAACTgtatgtttttgaccatatattttttattgtagttgttctgtttctttagattcatagacccc-ttggaggcaaccacatgattgtttcaaagagcgtaaggaagttgtattttggcattgatgaaatatcctgtctcag
upper sequence: PP1S357_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 5'ss of exon 10
AAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgta--ttaacatttggacttttgtttcgaaagaaaagacgtatagttatcgtttgagttcgcagcatgttgtgtactaagtttctggcattcttgtcatgac
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CAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGCCTATTATCACCCAACTgtaagttcttacttccattttt-ttccgttt-------tttgtagt-gtcgatgtaataaacttcaaaacttgggatcattctctag---------------
upper sequence: PP1S357_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT2G34410.1 (Arabidopsis thaliana), 5'ss of exon 9
-AAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgtattaacatttggacttttgtttcgaaagaaaagacgtatagttatcgtttgagttcgcagcatgttgtgtactaagtttctggcattcttgtcatgac
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TAAACCAGAACTACCACTT-TTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGCCTATTTCCATCCCACTgta-----------actcttgaacctacagccttctcgttttttcat-atcttctcatgaaccctacgattaaaatattttttgacattttcatttcag-
upper sequence: PP1S357_34V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT1G29890.2 (Arabidopsis thaliana), 5'ss of exon 8
-AAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgtattaacatttggacttttgtttcgaaagaaaagacgtatagttatcgtttgagttcgcagcatgttgtgtactaagtttctggcattcttgtcatgac
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TAAACCAGACCTTCCACGT-CTACACGAATGGCATTTCAGATCTGGACTTGATCGCTACATATGGATCATCGGCATGATATATGCATATTTTCATCCCACTgtaattcca---gaaccatggtgctttcattttttccatat--ctcctctcgaaagacgcaactaaatatattggggatttcag----------------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|208368050|gb|DC955429.1|DC955429EST: ATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACG GTAGAAAGGTGGCNTGAAAAGGTAGAGGAGATGGAGTACAAAAGAAGGACC
genomic: ATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgtattaacat ... atgttcgcagGTAGAAAGGTGGCTTGAAAAGGTAGAGGAGATGGAGTACAAAAGAAGGACC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgtattaacatttggacttttgtttcgaaagaaaagacgtatagttatcgtttgagttcgcagcatgttgtgtactaagtttctggcattcttgtcatgac
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