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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATACAACAAAGGTTGATGACCTTGTCAAGGATAAAATTGAAGCAACTGAAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttccttgtccatttcattattgatatgggcatgtccttaaataacttgcacgagatgtctgtactgtagaagtcatgaggaaagtagttctgctcacttgcactagtttacgaaccctggctgatgtttcgtatacctttctttgcag

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 29
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|162163791|gb|FC340338.1|FC340338
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162271743|gb|FC448876.1|FC448876
EST:     AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162227860|gb|FC403668.1|FC403668
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162160962|gb|FC337493.1|FC337493
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162243866|gb|FC423183.1|FC423183
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162195289|gb|FC369276.1|FC369276
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162192127|gb|FC368276.1|FC368276
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162150854|gb|FC327334.1|FC327334
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162243865|gb|FC423182.1|FC423182
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162243366|gb|FC417067.1|FC417067
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162150853|gb|FC327333.1|FC327333
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162243367|gb|FC417068.1|FC417068
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162211493|gb|FC387365.1|FC387365
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162256157|gb|FC432213.1|FC432213
EST:     AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162172579|gb|FC348624.1|FC348624
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162195262|gb|FC369275.1|FC369275
EST:     AAGAAAAGCGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
EST: gi|162271744|gb|FC448877.1|FC448877
EST:     AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAG                         AATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT
genomic: AAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCT

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: 17

GTATACAACAAAGGTTGATGACCTTGTCAAGGATAAAATTGAAGCAACTGAAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttcc ... ttctttgcagAATATGTATGCCCAGCTTTTGCCTTTAGCTCTACCTCCTCCTCCTGTTCCTGGTGTGAATGGCTTTGCGCCTGGCATGGGCATGCCTACCATGAGTGGTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATACAACAAAGGTTGATGACCTTGTCAAGGATAAAATTGAAGCAACTGAAGAAAAGAGGTCGAAGGAGTCCGAAGAGAAGGAGGTTGTGGCGCAACAGgtatatttccttgtccatttcattattgatatgggcatgtccttaaataacttgcacgagatgtctgtactgtagaagtcatgaggaaagtagttctgctcacttgcactagtttacgaaccctggctgatgtttcgtatacctttctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG