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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaccaattgctgtattggctcaattcagaagttccattcagttatggcaggtgcttatgcaggtgctgaatggattgatggccaaagtcatcctcatttagagtagatgtctataaacagaatttgtggaaggtttgatgtaccctgacccttgttgacggggatccctggctttactgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTTTTGGGCATGAC

Basic information

species Physcomitrella patens
transcript PP1S120_79V6.2
intron # 2
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|18342689|gb|BJ174724.1|BJ174724
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|67692817|gb|BJ953050.1|BJ953050
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|37821833|gb|BJ579899.1|BJ579899
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|67694462|gb|BJ954695.1|BJ954695
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|67574192|gb|BJ947016.1|BJ947016
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|162210552|gb|FC386848.1|FC386848
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|67569549|gb|BJ942373.1|BJ942373
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|162221907|gb|FC398175.1|FC398175
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|162227422|gb|FC403156.1|FC403156
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|162266890|gb|FC443004.1|FC443004
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
EST: gi|67697592|gb|BJ957825.1|BJ957825
EST:     ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACC                         ATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT
genomic: ATTGTGGCAGTCCTGATGCAGCCACCAAAAGCTACTATGTGCAACAAACCgtgagtacca ... tgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgatgtaccctgacccttgttgacggggatccctggctttactgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTTTTGGGCATGAC
                    tgttgac  putative branch site (score: 3)
                                       ctttact  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaccaattgctgtattggctcaattcagaagttccattcagttatggcaggtgcttatgcaggtgctgaatggattgatggccaaagtcatcctcatttagagtagatgtctataaacagaatttgtggaaggtttgatgtaccctgacccttgttgacggggatccctggctttactgctatccagATGTACAGAATCAAGGACCCCAAGGCAAGCTTGGAGTTCTACTCAAAGGTTTTGGGCATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG