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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttgacaaggctaaagtttcagtaggagattgttgcatcgcctttctttgcgacttgcgttcgtaatgctcggcgaaacttatattgtaagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGCTGGAATCTTTGGGCTAGCTTCTGGATTTTTTTGCGCAAAATTTTGATCT

Basic information

species Physcomitrella patens
transcript PP1S92_76V6.3
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|208380028|gb|DC914578.1|DC914578
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|67569956|gb|BJ942780.1|BJ942780
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|18350506|gb|BJ182557.1|BJ182557
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|18348078|gb|BJ180125.1|BJ180125
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|100445839|gb|CJ970138.1|CJ970138
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|100390301|gb|BY952709.1|BY952709
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|208360265|gb|DC943009.1|DC943009
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|67507727|gb|BJ940606.1|BJ940606
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|208389789|gb|DC938337.1|DC938337
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|208386851|gb|DC941569.1|DC941569
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|100399889|gb|BY990672.1|BY990672
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|67570064|gb|BJ942888.1|BJ942888
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|208366745|gb|DC931402.1|DC931402
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
EST: gi|18330584|gb|BJ162590.1|BJ162590
EST:     ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAG                         ATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC
genomic: ACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGC

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: 35 (upstream exon), 27 (downstream exon)
Score: 31

CTTGCTTTGTGTGGCTTCTCCAACGCGGCTCTCTGAACGCGCCTCCCTCAACGTCGTTGATCATCGATTTGTCGCTGCCACCGACTCCGCTTGCTTCCAGgtactgcact ... aagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGCTGGAATCTTTGGGCTAGCTTCTGGATTTTTTTGCGCAAAATTTTGATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttgcgacttgcgttcgtaatgctcggcgaaacttatattgtaagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGCTGGAATCTTTGGGCTAGCTTCTGGATTTTTTTGCGCAAAATTTTGATCT
                                aaacttatattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttgacaaggctaaagtttcagtaggagattgttgcatcgcctttctttgcgacttgcgttcgtaatgctcggcgaaacttatattgtaagactgtagATAAAGCTTTTCAGGAAGGATCAGAGGTGGGAGCGAGGGAGTTTCTGGGGCTGGAATCTTTGGGCTAGCTTCTGGATTTTTTTGCGCAAAATTTTGATCT

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