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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctttttttttccatggatttccagcgtacgtattgaaaatgtgttgtaaatcctacccttacaatgtgcttgatttgctcgccgccattttcacagttaacataattttttgttgcaatgtagatggcttagctggtggggagattcactaaatttatcatgtaccttatgcttttctcttgcag

Basic information

species Physcomitrella patens
transcript PP1S475_2V6.1
intron # 2
splice site 5'
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|100416912|gb|BY993150.1|BY993150
EST:     GANAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|18372909|gb|BJ204511.1|BJ204511
EST:     AAAGGACAAACGGAGATATTTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGGATGAGGTACTGTTGA
genomic: AAAGGACAAACGGAGATATTTT-GGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCG-ATGAGGTACTGTTGA
EST: gi|67578446|gb|BJ950613.1|BJ950613
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|162171220|gb|FC346378.1|FC346378
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|100447818|gb|CJ972117.1|CJ972117
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGANGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|67572167|gb|BJ944991.1|BJ944991
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|100363224|gb|BY984419.1|BY984419
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAGTCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|100372450|gb|BY985605.1|BY985605
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|67507761|gb|BJ940640.1|BJ940640
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|100445740|gb|CJ970039.1|CJ970039
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGANGTACTG
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTG
EST: gi|162276055|gb|FC452331.1|FC452331
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|162220129|gb|FC395406.1|FC395406
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|162222735|gb|FC398989.1|FC398989
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|18348573|gb|BJ180622.1|BJ180622
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|162160798|gb|FC336697.1|FC336697
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
EST: gi|100371055|gb|BY985916.1|BY985916
EST:     GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA                         GGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA
genomic: GAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 15

ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctt ... tctcttgcagGGGAATTTCAGAATCAGATGTTGAATCTTTTGTCGATGAGGTACTGTTGAAGGGGGACAAGTGGGCCTTAGGGGAATCTGAGCCTCTTGTTGGAACCCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAAgtgagtcctttttttttccatggatttccagcgtacgtattgaaaatgtgttgtaaatcctacccttacaatgtgcttgatttgctcgccgccattttcacagttaacataattttttgttgcaatgtagatggcttagctggtggggagattcactaaatttatcatgtaccttatgcttttctcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - GGAGAT