Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttgtctcagatagatataatcccgatgttttttttttttttttttttttatatttattttgacctcttttcgttttttcttaaatcagctccctaaggtacttcaagctgttttaatgactttgcatgatttctcttgcag

Basic information

species Physcomitrella patens
transcript PP1S41_288V6.1
intron # 2
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:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100362100|gb|BY966332.1|BY966332
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCTAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|208389785|gb|DC938333.1|DC938333
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|67574213|gb|BJ947037.1|BJ947037
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18367079|gb|BJ199159.1|BJ199159
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|162261873|gb|FC438397.1|FC438397
EST:     CTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: CTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|162208338|gb|FC384650.1|FC384650
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|67569697|gb|BJ942521.1|BJ942521
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18356720|gb|BJ188779.1|BJ188779
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18358000|gb|BJ190059.1|BJ190059
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18367904|gb|BJ199987.1|BJ199987
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18373417|gb|BJ204995.1|BJ204995
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|67507947|gb|BJ940822.1|BJ940822
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|67570034|gb|BJ942858.1|BJ942858
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18331944|gb|BJ163956.1|BJ163956
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100393083|gb|BY989735.1|BY989735
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100383314|gb|BY987055.1|BY987055
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|208368231|gb|DC931457.1|DC931457
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|22132263|gb|BQ827064.1|BQ827064
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100443023|gb|BY981649.1|BY981649
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18368770|gb|BJ200855.1|BJ200855
EST:     ACGATATTATCAGGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18343655|gb|BJ175693.1|BJ175693
EST:     CGATATTATCAAGCAAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: CGATATTATCAAGC-AGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18345702|gb|BJ177745.1|BJ177745
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100388445|gb|BY952047.1|BY952047
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18343615|gb|BJ175653.1|BJ175653
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18364030|gb|BJ196103.1|BJ196103
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100447071|gb|CJ971370.1|CJ971370
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100442970|gb|BY963465.1|BY963465
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|208389289|gb|DC933317.1|DC933317
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|208391882|gb|DC945961.1|DC945961
EST:     AGAAGGCTAACGCCAAAACTCGNATTCCG                         ATCAAAGGGAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: AGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100447799|gb|CJ972098.1|CJ972098
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100392179|gb|BY953233.1|BY953233
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18348521|gb|BJ180570.1|BJ180570
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100416674|gb|BY993031.1|BY993031
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100402967|gb|BY973441.1|BY973441
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|162261874|gb|FC438398.1|FC438398
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|18345749|gb|BJ177792.1|BJ177792
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
EST: gi|100383489|gb|BY950273.1|BY950273
EST:     ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCG                         ATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT
genomic: ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTT

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: 29 (upstream exon), 31 (downstream exon)
Score: 33

ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttg ... tctcttgcagATCAAAGGAAGAAATAAGACGCCAAACGCTCTTGCTGCTAAGGCTGCACTTCAAAAATCTGTTGCTGCTCGATCATCAGGCATGCGACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGATATTATCAAGCAGTCGAAGAAGGCTAACGCCAAAACTCGAATTCCGgtaagtgttgtctcagatagatataatcccgatgttttttttttttttttttttttatatttattttgacctcttttcgttttttcttaaatcagctccctaaggtacttcaagctgttttaatgactttgcatgatttctcttgcag

- - - - - - - - - CGAAGA
- - - - - - - - - - AAGAAG