Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctttggttgcagcatcgactgattgtcagggtgtatgtcatccttttcgttcggggaagctcaaattgcgtctgatgtgggtaacttggattccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTGAGCTCGTGGACCTAGGGGCCACCAAATTGCTGTGGCAGGCTTCAGGTTT

Basic information

species Physcomitrella patens
transcript PP1S49_283V6.3
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|18374636|gb|BJ206214.1|BJ206214
EST:     TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAG                         GTAACAGCGAGGGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
genomic: TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAGgtaagccagt ... attccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
EST: gi|67570207|gb|BJ943031.1|BJ943031
EST:     TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAAC---                         G----AGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
genomic: TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAGgtaagccagt ... attccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
EST: gi|18328592|gb|BJ160597.1|BJ160597
EST:     TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAG                         GTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
genomic: TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAGgtaagccagt ... attccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
EST: gi|100445902|gb|CJ970201.1|CJ970201
EST:     TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAG                         GTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
genomic: TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAGgtaagccagt ... attccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
EST: gi|67720034|gb|BJ970293.1|BJ970293
EST:     TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAG                         GTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
genomic: TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAGgtaagccagt ... attccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
EST: gi|18371273|gb|BJ202875.1|BJ202875
EST:     TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAG                         GTAACAGCGAGGGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
genomic: TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAGgtaagccagt ... attccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
EST: gi|18343174|gb|BJ175212.1|BJ175212
EST:     TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAG                         GTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG
genomic: TATTGTGAGTTCTACCTGCAGCGGGCCCTGCTCAGGCGGGTCAGAACGAGgtaagccagt ... attccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgttcggggaagctcaaattgcgtctgatgtgggtaacttggattccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTGAGCTCGTGGACCTAGGGGCCACCAAATTGCTGTGGCAGGCTTCAGGTTT
                                  gggtaac  putative branch site (score: 3)
                                              ttccatt  putative PPT
                tcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctttggttgcagcatcgactgattgtcagggtgtatgtcatccttttcgttcggggaagctcaaattgcgtctgatgtgggtaacttggattccattagGTAACAGCGAGAGAAGTGGAGAGAGTGAACACCTGACCATCTATTTTCGTGAGCTCGTGGACCTAGGGGCCACCAAATTGCTGTGGCAGGCTTCAGGTTT

- - - - tgcagca