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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttccgaattcctggaaacattattttgaattttttttcaaccacatcggtttgaatagcgattagggttgtccaggtagtgctcggtgctgtaaggaatctgggaattaaagtgcggtgagtgcgtggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGTTCCAGTTCCCTGAGGGTACAGTGGAGTTGTACGCTGAGAAGGTGAACAA

Basic information

species Physcomitrella patens
transcript PP1S41_146V6.1
intron # 2
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|208344994|gb|DC925404.1|DC925404
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162217138|gb|FC392502.1|FC392502
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162246681|gb|FC425274.1|FC425274
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|19788800|gb|BQ040933.1|BQ040933
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|19778407|gb|BQ039307.1|BQ039307
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162220065|gb|FC395385.1|FC395385
EST:     CTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|18341437|gb|BJ173472.1|BJ173472
EST:     ATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: ATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162259170|gb|FC435203.1|FC435203
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|67704473|gb|BJ964706.1|BJ964706
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162254129|gb|FC429653.1|FC429653
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|37823259|gb|BJ581325.1|BJ581325
EST:     TATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: TATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162230909|gb|FC406748.1|FC406748
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|67693697|gb|BJ953930.1|BJ953930
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162220064|gb|FC395384.1|FC395384
EST:     CTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162250244|gb|FC425495.1|FC425495
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162250245|gb|FC425496.1|FC425496
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162279949|gb|FC456135.1|FC456135
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162217139|gb|FC392503.1|FC392503
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162153703|gb|FC329106.1|FC329106
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162246682|gb|FC425275.1|FC425275
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|208367708|gb|DC947386.1|DC947386
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|67702691|gb|BJ962924.1|BJ962924
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAAGG
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAA-GG
EST: gi|208379087|gb|DC911612.1|DC911612
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|208389218|gb|DC933246.1|DC933246
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|7147663|gb|AW509634.1|AW509634
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162230908|gb|FC406747.1|FC406747
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|18332170|gb|BJ164183.1|BJ164183
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|67575972|gb|BJ948796.1|BJ948796
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162211611|gb|FC387691.1|FC387691
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|18344067|gb|BJ176106.1|BJ176106
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|67570422|gb|BJ943246.1|BJ943246
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
EST: gi|162153702|gb|FC329105.1|FC329105
EST:     CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGG                         GTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT
genomic: CATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGT

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: 98

CGGGAACTTGCCGAGGATGGCTACTCCGGCGTTGAAGTGCGCGTGACCCCCATGCGTACCGAAATTATCATCCGCGCTACTCGGACTCAGAATGTGTTGGgttagttccg ... tggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGTTCCAGTTCCCTGAGGGTACAGTGGAGTTGTACGCTGAGAAGGTGAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcggtgctgtaaggaatctgggaattaaagtgcggtgagtgcgtggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGTTCCAGTTCCCTGAGGGTACAGTGGAGTTGTACGCTGAGAAGGTGAACAA
                        aattaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttccgaattcctggaaacattattttgaattttttttcaaccacatcggtttgaatagcgattagggttgtccaggtagtgctcggtgctgtaaggaatctgggaattaaagtgcggtgagtgcgtggttggcagGTGAGAAGGGACGCAGGATCAGGGAATTGACATCCGTGGTACAGAAAAGGTTCCAGTTCCCTGAGGGTACAGTGGAGTTGTACGCTGAGAAGGTGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG