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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctttcattaggcatgtttcaggtgctcttgtttttttagcaagatcgattgtgtaaggtttttccatcgttatattaaaagttcacctttgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGGGTCGACCCAAAGAAAATGTTGGGACCATCATAGGCCCAGTCAAACTTAA

Basic information

species Physcomitrella patens
transcript PP1S49_154V6.1
intron # 16
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|37846628|gb|BJ604636.1|BJ604636
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162193052|gb|FC371476.1|FC371476
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162199788|gb|FC375861.1|FC375861
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37822641|gb|BJ580707.1|BJ580707
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37848238|gb|BJ606246.1|BJ606246
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|67724429|gb|BJ974688.1|BJ974688
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162169177|gb|FC345144.1|FC345144
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37845743|gb|BJ603751.1|BJ603751
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37848321|gb|BJ606329.1|BJ606329
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162170411|gb|FC347609.1|FC347609
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|18340439|gb|BJ172467.1|BJ172467
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37844446|gb|BJ602454.1|BJ602454
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37830591|gb|BJ588603.1|BJ588603
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37850973|gb|BJ608981.1|BJ608981
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|208369492|gb|DC955905.1|DC955905
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162152401|gb|FC327964.1|FC327964
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162169176|gb|FC345143.1|FC345143
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37844732|gb|BJ602740.1|BJ602740
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|18335537|gb|BJ167557.1|BJ167557
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162170412|gb|FC347610.1|FC347610
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162193053|gb|FC371477.1|FC371477
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|18334072|gb|BJ166088.1|BJ166088
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|208373600|gb|DC952425.1|DC952425
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|162199787|gb|FC375860.1|FC375860
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGTCTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37839892|gb|BJ597900.1|BJ597900
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
EST: gi|37844267|gb|BJ602275.1|BJ602275
EST:     AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG                         GAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG
genomic: AAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGG

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: 32 (upstream exon), 20 (downstream exon)
Score: 8

AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctc ... tgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGGGTCGACCCAAAGAAAATGTTGGGACCATCATAGGCCCAGTCAAACTTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgattgtgtaaggtttttccatcgttatattaaaagttcacctttgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGGGTCGACCCAAAGAAAATGTTGGGACCATCATAGGCCCAGTCAAACTTAA
                                     ttcaccttt  CT-rich tract
                         ttatattaaaagttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctttcattaggcatgtttcaggtgctcttgtttttttagcaagatcgattgtgtaaggtttttccatcgttatattaaaagttcacctttgttacgcagGAAGCTGCTATGAGTCTGGGCTATCTAACATCTGAAGAGTTTGATGAGTGGGTCGACCCAAAGAAAATGTTGGGACCATCATAGGCCCAGTCAAACTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA