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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtattactttccatctatgtctctgcctgtacatgcattttgctgacatctcataagtgtgtattttggacattgtctctgtaatctatcagcagtaggaacgccattttcttctgatacttggtctatcatttgattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCTTTAAGTTCGCTGGGAATCCAAATATTATTGTTGCTGTGAAAGCTTTTGG

Basic information

species Physcomitrella patens
transcript PP1S9_391V6.1
intron # 4
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|100363885|gb|BY966219.1|BY966219
EST:     TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTG                         GTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
genomic: TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
EST: gi|100355079|gb|BY964990.1|BY964990
EST:     TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTG                         GTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
genomic: TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
EST: gi|100441261|gb|BY962550.1|BY962550
EST:     TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTG                         GTATGAAAGTTTATGATACTAAGGAGGCATAGATGATTCTCGAGCCTTCCT
genomic: TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
EST: gi|100438381|gb|BY979928.1|BY979928
EST:     TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTG                         GTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
genomic: TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
EST: gi|162267810|gb|FC443800.1|FC443800
EST:     TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTG                         GTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
genomic: TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
EST: gi|162274567|gb|FC451010.1|FC451010
EST:     TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTG                         GTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
genomic: TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
EST: gi|100389520|gb|BY988998.1|BY988998
EST:     TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTG                         GTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
genomic: TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
EST: gi|100364726|gb|BY947877.1|BY947877
EST:     TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTG                         GTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT
genomic: TATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCT

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: 35 (upstream exon), 32 (downstream exon)
Score: 19

CAGGCACAGCCTTACATTGATAAATATGGGCCACAGTACAAGATGGATTCTATCGAGTTCCAGTCACTTACCTTGGGAACGTTGCCTCCTACATTTGTTGgtgcgtatta ... gattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCTTTAAGTTCGCTGGGAATCCAAATATTATTGTTGCTGTGAAAGCTTTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcagtaggaacgccattttcttctgatacttggtctatcatttgattttctagGTATGAAAGTTTATGATACTAAGGAGGCAGAGATGATTCTCGAGCCTTCCTTTAAGTTCGCTGGGAATCCAAATATTATTGTTGCTGTGAAAGCTTTTGG
                                               ttttct  CT-rich tract
                                     tatcatttgatttt  TA-rich tract