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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacacgaccttgatttatcatgcatgtgctactattttctttttatcgtggtaacagcacattgactaatgaactttatgcactgcaatggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAGGCTCTCGGTTGATCACCTGTGAAGCGGATAAGACCATCAAATTTTGGAA

Basic information

species Physcomitrella patens
transcript PP1S169_73V6.2
intron # 15
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|162203186|gb|FC379283.1|FC379283
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|162175454|gb|FC350924.1|FC350924
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37832005|gb|BJ590017.1|BJ590017
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37822469|gb|BJ580535.1|BJ580535
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37823397|gb|BJ581463.1|BJ581463
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|162183680|gb|FC359908.1|FC359908
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|162198129|gb|FC373079.1|FC373079
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37829624|gb|BJ587636.1|BJ587636
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37827542|gb|BJ585554.1|BJ585554
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|18336709|gb|BJ168732.1|BJ168732
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37841942|gb|BJ599950.1|BJ599950
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37829602|gb|BJ587614.1|BJ587614
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37834715|gb|BJ592727.1|BJ592727
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37828539|gb|BJ586551.1|BJ586551
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|67720614|gb|BJ970873.1|BJ970873
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|162266558|gb|FC442789.1|FC442789
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|162160838|gb|FC337660.1|FC337660
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|208365406|gb|DC950873.1|DC950873
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
EST: gi|37823750|gb|BJ581816.1|BJ581816
EST:     CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG                         GGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG
genomic: CTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAG

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: 25 (upstream exon), 33 (downstream exon)
Score: 5

GTGATAATGGAAGTATGTGGTTTTGGGACTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctacc ... ggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAGGCTCTCGGTTGATCACCTGTGAAGCGGATAAGACCATCAAATTTTGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgtggtaacagcacattgactaatgaactttatgcactgcaatggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAGGCTCTCGGTTGATCACCTGTGAAGCGGATAAGACCATCAAATTTTGGAA
                   gactaat  putative branch site (score: 5)
                           aactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacgaccttgatttatcatgcatgtgctactattttctttttatcgtggtaacagcacattgactaatgaactttatgcactgcaatggttttgtagGGTCTTTGGATAGCGAGGCTGGAATCTATGCTCTTTCATTTGATCAGACAGGCTCTCGGTTGATCACCTGTGAAGCGGATAAGACCATCAAATTTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC