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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtgcagtttatacaggcgtttttgcttgaagcaaacctggtcggtctacccgcacagacagcattcctcatttctcaatttttaataaacccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGAGAGAATCTTTGAAATCTCGTCATAGGCGTTTGAGGAAGAAG

Basic information

species Physcomitrella patens
transcript PP1S97_12V6.1
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|67573622|gb|BJ946446.1|BJ946446
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|18361696|gb|BJ193763.1|BJ193763
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|208377631|gb|DC932167.1|DC932167
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|37841451|gb|BJ599459.1|BJ599459
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162237052|gb|FC413211.1|FC413211
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162272082|gb|FC447876.1|FC447876
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162271630|gb|FC447515.1|FC447515
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|67574202|gb|BJ947026.1|BJ947026
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|208361024|gb|DC946671.1|DC946671
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162225027|gb|FC401443.1|FC401443
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|18363385|gb|BJ195457.1|BJ195457
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|37845987|gb|BJ603995.1|BJ603995
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|67507573|gb|BJ940454.1|BJ940454
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|67697007|gb|BJ957240.1|BJ957240
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|67693764|gb|BJ953997.1|BJ953997
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|208395976|gb|DC915736.1|DC915736
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162234108|gb|FC410543.1|FC410543
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162234312|gb|FC410058.1|FC410058
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162206486|gb|FC382855.1|FC382855
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162247010|gb|FC423952.1|FC423952
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162225028|gb|FC401444.1|FC401444
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|37839389|gb|BJ597397.1|BJ597397
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|67570482|gb|BJ943306.1|BJ943306
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162268056|gb|FC443526.1|FC443526
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
EST: gi|162234311|gb|FC410057.1|FC410057
EST:     GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAA                         CTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA
genomic: GGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGA

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: 26 (upstream exon), 31 (downstream exon)
Score: 23

ATGGCGTCGCTGTCGCTGAGAAGCTCTCCATTCACGGAATTCAACGGCTTGGCTGCAGCTCCTTCCTTCCGCCCTTCAATCCCTGCGCCCACACGCTCAAgtgagttttt ... acccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGAGAGAATCTTTGAAATCTCGTCATAGGCGTTTGAGGAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctacccgcacagacagcattcctcatttctcaatttttaataaacccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGAGAGAATCTTTGAAATCTCGTCATAGGCGTTTGAGGAAGAAG
                                    ttttaat  putative branch site (score: 23)
                                              cccttgc  putative PPT
                        tcatttctcaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtgcagtttatacaggcgtttttgcttgaagcaaacctggtcggtctacccgcacagacagcattcctcatttctcaatttttaataaacccttgcagCTTTGTTGCGGGAGACGTTGAAGGTAGAGGCTTTGAAGGATCAAACCCGGAGAGAATCTTTGAAATCTCGTCATAGGCGTTTGAGGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -ccgcaca