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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCCTTGTGTGACTGGGCTCATCATGGCGGAGTTCGATGTGCCTGCGGCGATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgcctcgtttgcccctgcaatttttttgtggtgcgtgtttctttaaatgttctgcagctgttaggattaactttgaatgctatctttctctga...

Basic information

species Physcomitrella patens
transcript PP1S41_288V6.1
intron # 1
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|100386941|gb|BY988210.1|BY988210
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|67576909|gb|BJ949733.1|BJ949733
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAG
EST: gi|100362100|gb|BY966332.1|BY966332
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|208389785|gb|DC938333.1|DC938333
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|67574213|gb|BJ947037.1|BJ947037
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18367079|gb|BJ199159.1|BJ199159
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|162208338|gb|FC384650.1|FC384650
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|67569697|gb|BJ942521.1|BJ942521
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18356720|gb|BJ188779.1|BJ188779
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18358000|gb|BJ190059.1|BJ190059
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18367904|gb|BJ199987.1|BJ199987
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18373417|gb|BJ204995.1|BJ204995
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|67507947|gb|BJ940822.1|BJ940822
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|67570034|gb|BJ942858.1|BJ942858
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18331944|gb|BJ163956.1|BJ163956
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100393083|gb|BY989735.1|BY989735
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100383314|gb|BY987055.1|BY987055
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|208368231|gb|DC931457.1|DC931457
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|22132263|gb|BQ827064.1|BQ827064
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100443023|gb|BY981649.1|BY981649
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18368770|gb|BJ200855.1|BJ200855
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAGGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18343655|gb|BJ175693.1|BJ175693
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGC-AGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18345702|gb|BJ177745.1|BJ177745
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100388445|gb|BY952047.1|BY952047
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18343615|gb|BJ175653.1|BJ175653
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18364030|gb|BJ196103.1|BJ196103
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100447071|gb|CJ971370.1|CJ971370
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100442970|gb|BY963465.1|BY963465
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|208389289|gb|DC933317.1|DC933317
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100447799|gb|CJ972098.1|CJ972098
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100392179|gb|BY953233.1|BY953233
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18348521|gb|BJ180570.1|BJ180570
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100416674|gb|BY993031.1|BY993031
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|100402967|gb|BY973441.1|BY973441
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|162261874|gb|FC438398.1|FC438398
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18345749|gb|BJ177792.1|BJ177792
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
EST: gi|18373871|gb|BJ205449.1|BJ205449
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGA
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGA
EST: gi|100383489|gb|BY950273.1|BY950273
EST:     GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTG                         ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG
genomic: GATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG

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: 34 (upstream exon), 35 (downstream exon)
Score: 38

GTGCCTTGTGTGACTGGGCTCATCATGGCGGAGTTCGATGTGCCTGCGGCGATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgc ... tattatgcagACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCCTTGTGTGACTGGGCTCATCATGGCGGAGTTCGATGTGCCTGCGGCGATGGACTTTTCTGTCGGCACGACAGAACAGAAGATGGATATGAGTCTTGgtacgtctgcctcgtttgcccctgcaatttttttgtggtgcgtgtttctttaaatgttctgcagctgttaggattaactttgaatgctatctttctctga

- - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA