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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatacttttctacaccaagagcatttgcagttttattgaacggaaaaccagcagaatgttgatactcggtgtctcaaccaccatgctttcttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAAGACGAGGTAGAAGAAGTTGCGCAGATCAAGGCATCCCACTTTGAAGAAG

Basic information

species Physcomitrella patens
transcript PP1S115_6V6.1
intron # 7
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|18340076|gb|BJ172104.1|BJ172104
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|67698180|gb|BJ958413.1|BJ958413
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162243139|gb|FC416739.1|FC416739
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162236747|gb|FC413426.1|FC413426
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|37828141|gb|BJ586153.1|BJ586153
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCCATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|37823927|gb|BJ581993.1|BJ581993
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162272739|gb|FC448365.1|FC448365
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|37839435|gb|BJ597443.1|BJ597443
EST:     AAATCTGTCAGCGCTCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|18333327|gb|BJ165341.1|BJ165341
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162157198|gb|FC332832.1|FC332832
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162250566|gb|FC428469.1|FC428469
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162272738|gb|FC448364.1|FC448364
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162255687|gb|FC431685.1|FC431685
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162236746|gb|FC413425.1|FC413425
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|18339619|gb|BJ171646.1|BJ171646
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|18337579|gb|BJ169603.1|BJ169603
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|37829568|gb|BJ587580.1|BJ587580
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|18340191|gb|BJ172219.1|BJ172219
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162163247|gb|FC339365.1|FC339365
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
EST: gi|162163246|gb|FC339364.1|FC339364
EST:     AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAG                         GATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA
genomic: AAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAA

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), 31 (downstream exon)
Score: 14

GGAAGCCCTGGCCAGGTACACACAAGGTTTCAGTGGTGCGGATATCACTGAAATCTGTCAGCGCGCTTGCAAGTACGCCATTCGTGAAAACATTGAGAAGgtaagttttt ... cttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAAGACGAGGTAGAAGAAGTTGCGCAGATCAAGGCATCCCACTTTGAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccagcagaatgttgatactcggtgtctcaaccaccatgctttcttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAAGACGAGGTAGAAGAAGTTGCGCAGATCAAGGCATCCCACTTTGAAGAAG
            tgttgat  putative branch site (score: 14)
                                         ctttcttatt  putative PPT
                                          tttcttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacttttctacaccaagagcatttgcagttttattgaacggaaaaccagcagaatgttgatactcggtgtctcaaccaccatgctttcttattgtagGATATTGAGAGGGAAAAGAGAATGGCAGAGAATCCCGAAGCTATGGAAGAAGACGAGGTAGAAGAAGTTGCGCAGATCAAGGCATCCCACTTTGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG