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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccagattgtcacaagttattgttttatagatggagaaattctaccctcaaaaccaacctgaggcatgctcacttacccttatcaatgtggcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATCGGTCGCCGCATAAAGAAG

Basic information

species Physcomitrella patens
transcript PP1S90_220V6.2
intron # 7
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|67572621|gb|BJ945445.1|BJ945445
EST:     GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAA                         CATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
genomic: GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAAgtaagttctt ... gcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
EST: gi|162173818|gb|FC349410.1|FC349410
EST:     GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAA                         CATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
genomic: GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAAgtaagttctt ... gcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
EST: gi|162169383|gb|FC345739.1|FC345739
EST:     GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAA                         CATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
genomic: GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAAgtaagttctt ... gcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
EST: gi|162152901|gb|FC329203.1|FC329203
EST:     GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAA                         CATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
genomic: GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAAgtaagttctt ... gcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
EST: gi|162186918|gb|FC362596.1|FC362596
EST:     GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAA                         CATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
genomic: GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAAgtaagttctt ... gcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
EST: gi|67717954|gb|BJ968213.1|BJ968213
EST:     GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAA                         CATTGCGGCGTGC
genomic: GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAAgtaagttctt ... gcgcgtgcagCATTGCGGCGTGC
EST: gi|162193418|gb|FC368917.1|FC368917
EST:     GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAA                         CATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC
genomic: GAGATGCTGGTTATCAGGATACATTGGAATGTGTCGCTGCTGTTGCTAAAgtaagttctt ... gcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcaaaaccaacctgaggcatgctcacttacccttatcaatgtggcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATCGGTCGCCGCATAAAGAAG
                         cacttac  putative branch site (score: 2)
                                  ttatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccagattgtcacaagttattgttttatagatggagaaattctaccctcaaaaccaacctgaggcatgctcacttacccttatcaatgtggcgcgtgcagCATTGCGGCGTGCCAGAAGGAGCCGTTCTCATCGAATCAACTGGAGTCATCGGTCGCCGCATAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG