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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtatggtctcccctggatggattgaagagttggttggaattgaagtgtctctcttaggtatttatgtcggatgactcatgtcagtttcttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTG

Basic information

species Physcomitrella patens
transcript PP1S44_58V6.1
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|37837834|gb|BJ595842.1|BJ595842
EST:     CTCAAGGATGAG                         AAACTGGGGCAACATCANCCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: CTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|18341570|gb|BJ173605.1|BJ173605
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|37851441|gb|BJ609449.1|BJ609449
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|162233564|gb|FC410946.1|FC410946
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|208383033|gb|DC927783.1|DC927783
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|18363127|gb|BJ195199.1|BJ195199
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|37849290|gb|BJ607298.1|BJ607298
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|18324822|gb|BJ156817.1|BJ156817
EST:     GTCTTGACAATGCCGGGAAGACNACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|67569045|gb|BJ941869.1|BJ941869
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|67692279|gb|BJ952512.1|BJ952512
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|208349652|gb|DC917830.1|DC917830
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|37841128|gb|BJ599136.1|BJ599136
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|162262185|gb|FC437928.1|FC437928
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|162260872|gb|FC437929.1|FC437929
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|18375235|gb|BJ206813.1|BJ206813
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|162233563|gb|FC410945.1|FC410945
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|37840342|gb|BJ598350.1|BJ598350
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|162214418|gb|FC391177.1|FC391177
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|208363206|gb|DC954378.1|DC954378
EST:     GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
EST: gi|18339760|gb|BJ171787.1|BJ171787
EST:     GTCTTGACAATGCCGGGAAGNCNACACTTCTGCACATGCTCAAGGATGAG                         AAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC
genomic: GTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGC

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), 35 (downstream exon)
Score: 70

TCTTGCGAGCATAGGTTTGTGGCAGAAGGAGGCCAAAATCTTGTTCCTGGGTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctcccct ... ttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtctctcttaggtatttatgtcggatgactcatgtcagtttcttgtgaacagAAACTGGGGCAACATCAACCAACGCAGTATCCAACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTG
                                         tttcttgt  CT-rich tract
               tatttatgt  TA-rich tract