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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTTTTTGCAAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatccctacttgttgagacttaatgtagcaattccctcatcatactcacacaggaaaaaaaaaaaaaaaaaaaaaaaaagaagaagaatggctga...

Basic information

species Physcomitrella patens
transcript PP1S99_220V6.1
intron # 14
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|162163777|gb|FC340337.1|FC340337
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162196059|gb|FC372204.1|FC372204
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|37850455|gb|BJ608463.1|BJ608463
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTNTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|37847724|gb|BJ605732.1|BJ605732
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTNTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|37839128|gb|BJ597136.1|BJ597136
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162209584|gb|FC385888.1|FC385888
EST:     CAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: CAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162165452|gb|FC342019.1|FC342019
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162239475|gb|FC414040.1|FC414040
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162154186|gb|FC330317.1|FC330317
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTTTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162196058|gb|FC372203.1|FC372203
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|37845408|gb|BJ603416.1|BJ603416
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162154185|gb|FC330316.1|FC330316
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTTTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162266580|gb|FC442798.1|FC442798
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162266579|gb|FC442797.1|FC442797
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162158051|gb|FC334452.1|FC334452
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162239476|gb|FC414041.1|FC414041
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|37852138|gb|BJ610146.1|BJ610146
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
EST: gi|162162417|gb|FC339174.1|FC339174
EST:     AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAG                         CTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT
genomic: AAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTT

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), 34 (downstream exon)
Score: 13

GCTTTTTTTGCAAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatcc ... aaaactgcagCTGGGTTCCAAAATGAAGTTAACAGTGTTCAGATCAGAGTCCACTGGTGTTGCTCTCAAAGGCTGGGCAAAGTCAGCAAAGAAGAGGCACAGTCATCCGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTTTTTGCAAATCCTATGCAGTGTCAGCACTTTGCCTCTCTATGCCCTTGTCACTCAGgtactcatccctacttgttgagacttaatgtagcaattccctcatcatactcacacaggaaaaaaaaaaaaaaaaaaaaaaaaagaagaagaatggctga

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaagaa