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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaaggaatcagcatcatatggacgtagccatagctagcagtcacttcattacgaattaaaggtgggaaaggattgaaagatttcccgtttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGAAATCACTTGCGCCTGACCCTAACGCAATTGATCAAGGACCTACAGAGAA

Basic information

species Physcomitrella patens
transcript PP1S97_287V6.1
intron # 1
splice site 3'
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|162200892|gb|FC377087.1|FC377087
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|100365116|gb|BY966818.1|BY966818
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|18332453|gb|BJ164466.1|BJ164466
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAG
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAG
EST: gi|162280434|gb|FC456347.1|FC456347
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|100407039|gb|BY973977.1|BY973977
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|18371765|gb|BJ203367.1|BJ203367
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACG
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACG
EST: gi|67709712|gb|BJ965528.1|BJ965528
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|162155583|gb|FC331534.1|FC331534
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|162220086|gb|FC397031.1|FC397031
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|18366171|gb|BJ198249.1|BJ198249
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGC
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGC
EST: gi|18365896|gb|BJ197974.1|BJ197974
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|100395338|gb|BY953687.1|BY953687
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|162265304|gb|FC440422.1|FC440422
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
EST: gi|162267601|gb|FC444664.1|FC444664
EST:     TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAG                         GAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA
genomic: TTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGA

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: 33 (upstream exon), 19 (downstream exon)
Score: 2

AGGAGCAATGGCGCGGGCATGGACATCGAATGCAACAACCAGGGAGCTATTTTCGTGGAGGCCCACGCTACAGCAACGCTTGAAGATTTACTGAAATCAGgtacttctca ... ttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGAAATCACTTGCGCCTGACCCTAACGCAATTGATCAAGGACCTACAGAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcattacgaattaaaggtgggaaaggattgaaagatttcccgtttcgatgcagGAAACAGCAGTGCACGAGGTAGGGATACGTTTCAGCCGAGTCCGTTGTGGAAATCACTTGCGCCTGACCCTAACGCAATTGATCAAGGACCTACAGAGAA
                                     tttcccgtttc  CT-rich tract
          aattaaa  TA-rich tract