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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgcagttattgcttgcatttgactgccgattggaggccatgtccatcctcgcagatttgagctaatttgatacgaacttctttggacattgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGTGTCTCAGGAAAGTCCTGGCAGCAGAGCTTCACTGAAGCAGTGCAACGGA

Basic information

species Physcomitrella patens
transcript PP1S6_39V6.2
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|208375610|gb|DC902827.1|DC902827
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGCAG                       
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--GC-Ggtctgtgact ... attgcagc
EST: gi|100414271|gb|BY992695.1|BY992695
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         GCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
EST: gi|100368669|gb|BY967118.1|BY967118
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGCAG                       
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--GC-Ggtctgtgact ... attgcagc
EST: gi|208370406|gb|DC936412.1|DC936412
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         GCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
EST: gi|100384482|gb|BY987341.1|BY987341
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100384482|gb|BY987341.1|BY987341
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100384482|gb|BY987341.1|BY987341
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18355248|gb|BJ187307.1|BJ187307
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         GCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
EST: gi|100422995|gb|BY958103.1|BY958103
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGCAG                       
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--GC-Ggtctgtgact ... attgcagc
EST: gi|100414899|gb|BY956917.1|BY956917
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100414899|gb|BY956917.1|BY956917
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100414899|gb|BY956917.1|BY956917
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18342600|gb|BJ174635.1|BJ174635
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18342600|gb|BJ174635.1|BJ174635
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18342600|gb|BJ174635.1|BJ174635
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|208384726|gb|DC915273.1|DC915273
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGCAG                       
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--GC-Ggtctgtgact ... attgcagc
EST: gi|100450314|gb|CJ974201.1|CJ974201
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100450314|gb|CJ974201.1|CJ974201
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100450314|gb|CJ974201.1|CJ974201
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|208391626|gb|DC938239.1|DC938239
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGCAG                       
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--GC-Ggtctgtgact ... attgcagc
EST: gi|18348041|gb|BJ180088.1|BJ180088
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGCAG                       
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--GC-Ggtctgtgact ... attgcagc
EST: gi|18331659|gb|BJ163670.1|BJ163670
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18331659|gb|BJ163670.1|BJ163670
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18331659|gb|BJ163670.1|BJ163670
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|67704237|gb|BJ964470.1|BJ964470
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|67704237|gb|BJ964470.1|BJ964470
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|67704237|gb|BJ964470.1|BJ964470
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18347888|gb|BJ179935.1|BJ179935
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18347888|gb|BJ179935.1|BJ179935
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18347888|gb|BJ179935.1|BJ179935
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|208398027|gb|DC908199.1|DC908199
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         GCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
EST: gi|67718597|gb|BJ968856.1|BJ968856
EST:     GAGTGGATGGAGCGGTTGTGACCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|67718597|gb|BJ968856.1|BJ968856
EST:     GAGTGGATGGAGCGGTTGTGACCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|67718597|gb|BJ968856.1|BJ968856
EST:     GAGTGGATGGAGCGGTTGTGACCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100449094|gb|CJ973393.1|CJ973393
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         GCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
EST: gi|208387825|gb|DC941394.1|DC941394
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         GCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
EST: gi|208357483|gb|DC910566.1|DC910566
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|208357483|gb|DC910566.1|DC910566
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|208357483|gb|DC910566.1|DC910566
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100414206|gb|BY992663.1|BY992663
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100414206|gb|BY992663.1|BY992663
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100414206|gb|BY992663.1|BY992663
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100376271|gb|BY986105.1|BY986105
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100376271|gb|BY986105.1|BY986105
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100376271|gb|BY986105.1|BY986105
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|18352102|gb|BJ184156.1|BJ184156
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGCAG                       
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--GC-Ggtctgtgact ... attgcagc
EST: gi|100417664|gb|BY975593.1|BY975593
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGCAG                       
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAA--GC-Ggtctgtgact ... attgcagc
EST: gi|67716728|gb|BJ966988.1|BJ966988
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|67716728|gb|BJ966988.1|BJ966988
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|67716728|gb|BJ966988.1|BJ966988
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100443343|gb|BY963639.1|BY963639
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100443343|gb|BY963639.1|BY963639
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100443343|gb|BY963639.1|BY963639
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         C
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcag-
EST: gi|100375001|gb|BY949146.1|BY949146
EST:     GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCG                         GCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT
genomic: GAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGT

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), 34 (downstream exon)
Score: 11

GGGCTTTGGCAGGCATTTCAACTATTTTGAGACTGCGAGCTTTCCCCATCGAGTGGATGGAGCGGTTGTGGCCACTACATTCGGCGACCCTGCGAAAGCGgtctgtgact ... attgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGTGTCTCAGGAAAGTCCTGGCAGCAGAGCTTCACTGAAGCAGTGCAACGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatcctcgcagatttgagctaatttgatacgaacttctttggacattgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGTGTCTCAGGAAAGTCCTGGCAGCAGAGCTTCACTGAAGCAGTGCAACGGA
                    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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgcagttattgcttgcatttgactgccgattggaggccatgtccatcctcgcagatttgagctaatttgatacgaacttctttggacattgcagcagGCGTTTACTGTGAACCTCCTGCGAAGAGATCAACATGAGAAGCTCGCCGGTGTCTCAGGAAAGTCCTGGCAGCAGAGCTTCACTGAAGCAGTGCAACGGA

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