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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttattgcagttattgcttgcatttgactgccgattggaggccatgtccatcctcgcagatttgagctaatttgatacgaacttctttggacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGTGTCTCAGGAAAGTCCTGGCAGCAGAGCTTCACTGAAGCAGTGCAAC

Basic information

species Physcomitrella patens
transcript PP1S6_39V6.1
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|100414206|gb|BY992663.1|BY992663
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100414899|gb|BY956917.1|BY956917
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100368669|gb|BY967118.1|BY967118
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|67717327|gb|BJ967586.1|BJ967586
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CANGCNTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|18355248|gb|BJ187307.1|BJ187307
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         --G-CGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|67716728|gb|BJ966988.1|BJ966988
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100376271|gb|BY986105.1|BY986105
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|208375610|gb|DC902827.1|DC902827
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100443343|gb|BY963639.1|BY963639
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|18348041|gb|BJ180088.1|BJ180088
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|208384726|gb|DC915273.1|DC915273
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|208357483|gb|DC910566.1|DC910566
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|208387825|gb|DC941394.1|DC941394
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         --G-CGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100417664|gb|BY975593.1|BY975593
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100422995|gb|BY958103.1|BY958103
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100375001|gb|BY949146.1|BY949146
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--G                         C-GGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|208398027|gb|DC908199.1|DC908199
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         --G-CGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|18342600|gb|BJ174635.1|BJ174635
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100384482|gb|BY987341.1|BY987341
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|18331659|gb|BJ163670.1|BJ163670
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100450314|gb|CJ974201.1|CJ974201
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|18352102|gb|BJ184156.1|BJ184156
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|208370406|gb|DC936412.1|DC936412
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         --G-CGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|100414271|gb|BY992695.1|BY992695
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--G                         C-GGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|208391626|gb|DC938239.1|DC938239
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|67718597|gb|BJ968856.1|BJ968856
EST:     GAGTGGATGGAGCGGTTGTGACCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAG
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAG
EST: gi|100449094|gb|CJ973393.1|CJ973393
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--G                         C-GGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|18347888|gb|BJ179935.1|BJ179935
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
EST: gi|67704237|gb|BJ964470.1|BJ964470
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         CAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... gacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtccatcctcgcagatttgagctaatttgatacgaacttctttggacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGTGTCTCAGGAAAGTCCTGGCAGCAGAGCTTCACTGAAGCAGTGCAAC
                       taatttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttattgcagttattgcttgcatttgactgccgattggaggccatgtccatcctcgcagatttgagctaatttgatacgaacttctttggacattgcagCAGGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGTGTCTCAGGAAAGTCCTGGCAGCAGAGCTTCACTGAAGCAGTGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC