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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagatacactaatcgtgaaacagaagagagctccccacgaattcagagacacgaatgtctctcactctcgatttgatattctcttgtaatgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAGCGCTTGCTTATGGTACAATCGCAGCAACGATGCTGGTTGGACTCGCCAA

Basic information

species Physcomitrella patens
transcript PP1S485_2V6.3
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|100379676|gb|BY949888.1|BY949888
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|18356091|gb|BJ188150.1|BJ188150
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100410297|gb|BY992036.1|BY992036
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|162159250|gb|FC335103.1|FC335103
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTAACATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTGGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208347492|gb|DC909771.1|DC909771
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100421006|gb|BY993569.1|BY993569
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100419722|gb|BY957690.1|BY957690
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100401340|gb|BY990953.1|BY990953
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|208350029|gb|DC910264.1|DC910264
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18361207|gb|BJ193272.1|BJ193272
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|162270839|gb|FC446868.1|FC446868
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18368542|gb|BJ200627.1|BJ200627
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|100431820|gb|BY978522.1|BY978522
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|208348000|gb|DC905323.1|DC905323
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|100357038|gb|BY983663.1|BY983663
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|18365780|gb|BJ197858.1|BJ197858
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|18354959|gb|BJ187018.1|BJ187018
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|18343504|gb|BJ175542.1|BJ175542
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208383770|gb|DC911480.1|DC911480
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100400045|gb|BY990751.1|BY990751
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|67577633|gb|BJ949800.1|BJ949800
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100408577|gb|BY974194.1|BY974194
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|208383925|gb|DC907316.1|DC907316
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100361681|gb|BY947769.1|BY947769
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|100415879|gb|BY956969.1|BY956969
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAG                         AGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAG
EST: gi|18351413|gb|BJ183465.1|BJ183465
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a
EST: gi|208388919|gb|DC932947.1|DC932947
EST:     TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGGTTAATAGAG                
genomic: TCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCA---T----TT--TA-AGgttaatagag ... a

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: 17 (upstream exon), 19 (downstream exon)
Score: 1

GTGTCCACAGTCTTCTTTCTCCTGCAGCAGTTCCATTTTCTAGTGATCGTTCATGCTGGTGCCACGAGAGCCAAAGCTCGCACGTCCTTATCATTTTAAGgttaatagag ... atgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAGCGCTTGCTTATGGTACAATCGCAGCAACGATGCTGGTTGGACTCGCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagagacacgaatgtctctcactctcgatttgatattctcttgtaatgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAGCGCTTGCTTATGGTACAATCGCAGCAACGATGCTGGTTGGACTCGCCAA
                           atttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagatacactaatcgtgaaacagaagagagctccccacgaattcagagacacgaatgtctctcactctcgatttgatattctcttgtaatgtggacagAGATGGCGGCGGTCTTCAGAAATTCGAAGTTTAGTGTAAACGTCAATTTAGCGCTTGCTTATGGTACAATCGCAGCAACGATGCTGGTTGGACTCGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG