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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcccgaaacctggattttcagcatgatgaggttgcaggtgcaggtgttgctctgtcatttgaaatttctttacgcagggaattgaaatagttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGGTAGGCGCCCCGGAAGCTTTGGTGATAGGCGTGGTGGC

Basic information

species Physcomitrella patens
transcript PP1S93_67V6.1
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|208384568|gb|DC907069.1|DC907069
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... ttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
EST: gi|208375976|gb|DC906967.1|DC906967
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... ttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
EST: gi|100426838|gb|BY977388.1|BY977388
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCC----                         G---TG-----GGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... ttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
EST: gi|18357094|gb|BJ189153.1|BJ189153
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... ttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
EST: gi|18328441|gb|BJ160446.1|BJ160446
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... ttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
EST: gi|22491833|gb|BU051756.1|BU051756
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... ttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgctctgtcatttgaaatttctttacgcagggaattgaaatagttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGGTAGGCGCCCCGGAAGCTTTGGTGATAGGCGTGGTGGC
           atttgaaatttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcccgaaacctggattttcagcatgatgaggttgcaggtgcaggtgttgctctgtcatttgaaatttctttacgcagggaattgaaatagttgtgcttagGTTTTGCATCAGGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGGTAGGCGCCCCGGAAGCTTTGGTGATAGGCGTGGTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG