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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCCTTACCGAATTTTTCTCCGCCAAACCCGAGGAGCGTAGCGGTATTCTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgcaaatgtttttggtgtctgaacttgggaaatcccttattgcatctcaatagattaaatttatcttaattgttttggttcgtgcatcatactctttctgttctgttctacag

Basic information

species Physcomitrella patens
transcript PP1S201_115V6.3
intron # 9
splice site 5'
intron type U2

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|37846632|gb|BJ604640.1|BJ604640
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208385376|gb|DC956616.1|DC956616
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|22492293|gb|BU052216.1|BU052216
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|37847154|gb|BJ605162.1|BJ605162
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|37835612|gb|BJ593624.1|BJ593624
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|22132035|gb|BQ826945.1|BQ826945
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|37833789|gb|BJ591801.1|BJ591801
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208393949|gb|DC928729.1|DC928729
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|37821752|gb|BJ579818.1|BJ579818
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|37825580|gb|BJ583646.1|BJ583646
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208397894|gb|DC916649.1|DC916649
EST:     CTTTCTAAGGGAGGGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208385667|gb|DC952828.1|DC952828
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208380848|gb|DC923330.1|DC923330
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208356156|gb|DC957316.1|DC957316
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|67692042|gb|BJ952275.1|BJ952275
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|37853039|gb|BJ611047.1|BJ611047
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208393538|gb|DC949700.1|DC949700
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|37845884|gb|BJ603892.1|BJ603892
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|67725662|gb|BJ975921.1|BJ975921
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208381758|gb|DC928421.1|DC928421
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|37840656|gb|BJ598664.1|BJ598664
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208354258|gb|DC957450.1|DC957450
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|67722506|gb|BJ972765.1|BJ972765
EST:     AAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCNTTGAAGAGCATCATTGATAAAGGTGA
genomic: AAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
EST: gi|208348693|gb|DC926368.1|DC926368
EST:     CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGG                         GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA
genomic: CTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 22 (downstream exon)
Score: 23

ATATCCTTACCGAATTTTTCTCCGCCAAACCCGAGGAGCGTAGCGGTATTCTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgc ... tgttctacagGTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGAAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCCTTACCGAATTTTTCTCCGCCAAACCCGAGGAGCGTAGCGGTATTCTTTCTAAGGGAGAGGAAACAGCTGTCAGCCTGGAAGGGAAAGCAGCCGGgtacgattgcaaatgtttttggtgtctgaacttgggaaatcccttattgcatctcaatagattaaatttatcttaattgttttggttcgtgcatcatactctttctgttctgttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG