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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatcaaggatcatacccagtctttaataggagtgcccatgtcgccgttcccttcttgtactgtcgataatgatgttcttacgatgctcgtttct...

Basic information

species Physcomitrella patens
transcript PP1S40_14V6.1
intron # 6
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|162190539|gb|FC366177.1|FC366177
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162276038|gb|FC452314.1|FC452314
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162204488|gb|FC381716.1|FC381716
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|67699996|gb|BJ960229.1|BJ960229
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|67693939|gb|BJ954172.1|BJ954172
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162191409|gb|FC368179.1|FC368179
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|37837429|gb|BJ595437.1|BJ595437
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162276039|gb|FC452315.1|FC452315
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162204214|gb|FC379687.1|FC379687
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTTTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|208358113|gb|DC946741.1|DC946741
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|18341604|gb|BJ173639.1|BJ173639
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|7648089|gb|AW739072.1|AW739072
EST:     CCGAGGCAGCTGCTANGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTG
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTG
EST: gi|162186279|gb|FC361587.1|FC361587
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCT
EST: gi|162191408|gb|FC368178.1|FC368178
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162186278|gb|FC361586.1|FC361586
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|18339226|gb|BJ171253.1|BJ171253
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162206261|gb|FC382331.1|FC382331
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162279658|gb|FC455384.1|FC455384
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTTTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|37826197|gb|BJ584209.1|BJ584209
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|18336148|gb|BJ168170.1|BJ168170
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162205698|gb|FC381900.1|FC381900
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|208382842|gb|DC923889.1|DC923889
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162167193|gb|FC342758.1|FC342758
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
EST: gi|162205699|gb|FC381901.1|FC381901
EST:     CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG                         GTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT
genomic: CCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGT

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), 33 (downstream exon)
Score: 27

GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatc ... ttttgtgcagGTTGGATTTGGTGTAGGAAACGATTTCTCTACGGTCGCTGACGATTTGGGTATCGATAACCTTGAATCCTTGAATGCATCAGTCGAGGAAACAGCAGTTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAGgtatgaaatcaaggatcatacccagtctttaataggagtgcccatgtcgccgttcccttcttgtactgtcgataatgatgttcttacgatgctcgtttct

- - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT