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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgtgtaactaagcctttgggactgcagtaccttaaagttcgagctgttcctctctgagagaggcaagtcctgatgctaattgtgaaagtttgtctctcacgtatcatctaatcgttctattttggtgatgttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCAACCCAGAGAGTGGGCACCGTTCCTTTTGAATTTTGTATGTGCAGATTGG

Basic information

species Physcomitrella patens
transcript PP1S70_130V6.2
intron # 5
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|37832378|gb|BJ590390.1|BJ590390
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|67697161|gb|BJ957394.1|BJ957394
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162278351|gb|FC454229.1|FC454229
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCANACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCNCAAA-GCTTTTATGC
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATC-CAAAAGCTTTTATGC
EST: gi|37830446|gb|BJ588458.1|BJ588458
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTCTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|22132254|gb|BQ827059.1|BQ827059
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37843625|gb|BJ601633.1|BJ601633
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162275814|gb|FC451375.1|FC451375
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|67508075|gb|BJ940946.1|BJ940946
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162203104|gb|FC378499.1|FC378499
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCANACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37836257|gb|BJ594265.1|BJ594265
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162203103|gb|FC378498.1|FC378498
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162194745|gb|FC371592.1|FC371592
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|67694960|gb|BJ955193.1|BJ955193
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37833638|gb|BJ591650.1|BJ591650
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37828401|gb|BJ586413.1|BJ586413
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37823831|gb|BJ581897.1|BJ581897
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162278350|gb|FC454228.1|FC454228
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37827775|gb|BJ585787.1|BJ585787
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|67579405|gb|BJ951526.1|BJ951526
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|67694966|gb|BJ955199.1|BJ955199
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37851802|gb|BJ609810.1|BJ609810
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37838283|gb|BJ596291.1|BJ596291
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162275815|gb|FC451376.1|FC451376
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162276716|gb|FC452710.1|FC452710
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37843693|gb|BJ601701.1|BJ601701
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162239493|gb|FC416827.1|FC416827
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|67700339|gb|BJ960572.1|BJ960572
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATNCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|67697926|gb|BJ958159.1|BJ958159
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|18333899|gb|BJ165915.1|BJ165915
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162230342|gb|FC406906.1|FC406906
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|37845981|gb|BJ603989.1|BJ603989
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162276715|gb|FC452709.1|FC452709
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAG                         GCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCA
EST: gi|162239494|gb|FC416828.1|FC416828
EST:     AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCANACAAG                         GCATAATTGTTGTTGGCT
genomic: AGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCT

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), 34 (downstream exon)
Score: 21

AGCACCTGTGCAACTTCCGGAGAGGGTCTGTATGAAGGCCTTGACTGGCTGTCAAGTAACATCGCAAACAAGgtatattgtg ... ttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCAACCCAGAGAGTGGGCACCGTTCCTTTTGAATTTTGTATGTGCAGATTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttgtctctcacgtatcatctaatcgttctattttggtgatgttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCAACCCAGAGAGTGGGCACCGTTCCTTTTGAATTTTGTATGTGCAGATTGG
                    atctaat  putative branch site (score: 21)
                                           tgttttct  putative PPT
                             ttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattgtgtaactaagcctttgggactgcagtaccttaaagttcgagctgttcctctctgagagaggcaagtcctgatgctaattgtgaaagtttgtctctcacgtatcatctaatcgttctattttggtgatgttttctgcagGCATAATTGTTGTTGGCTAGTTCTGTGTTTTCATCCAAAAGCTTTTATGCAACCCAGAGAGTGGGCACCGTTCCTTTTGAATTTTGTATGTGCAGATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT