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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgtttcttatttgactctaaattgtgatttgcttagtccagtcgtgattttttcacaccaccgttttctgtatgtggttttagctgtccatttgtcccgcacaagttatttcaaacataggaagagtagttttctaatggatggtattgggatgcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTTGTGGGCATTGAAGCTAATCGCAACCATATTGATAATTTGATGCGAAGG

Basic information

species Physcomitrella patens
transcript PP1S49_154V6.1
intron # 13
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:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162193052|gb|FC371476.1|FC371476
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162199788|gb|FC375861.1|FC375861
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37822641|gb|BJ580707.1|BJ580707
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37848238|gb|BJ606246.1|BJ606246
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|67724429|gb|BJ974688.1|BJ974688
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTCGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162169177|gb|FC345144.1|FC345144
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37845743|gb|BJ603751.1|BJ603751
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37848321|gb|BJ606329.1|BJ606329
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162170411|gb|FC347609.1|FC347609
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|18340439|gb|BJ172467.1|BJ172467
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37844446|gb|BJ602454.1|BJ602454
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37850973|gb|BJ608981.1|BJ608981
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|208369492|gb|DC955905.1|DC955905
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162152401|gb|FC327964.1|FC327964
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162169176|gb|FC345143.1|FC345143
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37844732|gb|BJ602740.1|BJ602740
EST:     TTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: TTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|18335537|gb|BJ167557.1|BJ167557
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162170412|gb|FC347610.1|FC347610
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162193053|gb|FC371477.1|FC371477
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|18334072|gb|BJ166088.1|BJ166088
EST:     AACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: AACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|208373600|gb|DC952425.1|DC952425
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|162199787|gb|FC375860.1|FC375860
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37839892|gb|BJ597900.1|BJ597900
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT
EST: gi|37844267|gb|BJ602275.1|BJ602275
EST:     ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAG                         TCAATGGTGTTGCTTGGAGACGCCGCGGAGTCTTTCAGGAAGAACTGTGTT
genomic: ACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTT

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: 24 (upstream exon), 12 (downstream exon)
Score: 1

GTAATGGGTAACCATACTACCATTACAGTAGCGGGTTCTAATGGGCACTTTGAACTCAATGTTTACAAGCCTGTCATGATCAACGCTTTGCTTCAGgtacgtgttt ... gcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTTGTGGGCATTGAAGCTAATCGCAACCATATTGATAATTTGATGCGAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaaacataggaagagtagttttctaatggatggtattgggatgcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTTGTGGGCATTGAAGCTAATCGCAACCATATTGATAATTTGATGCGAAGG
                       ttctaat  putative branch site (score: 1)
                     ttttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgtttcttatttgactctaaattgtgatttgcttagtccagtcgtgattttttcacaccaccgttttctgtatgtggttttagctgtccatttgtcccgcacaagttatttcaaacataggaagagtagttttctaatggatggtattgggatgcatatgcagTCAATGGTGTTGCTTGGAGACGCCGCAGAGTCTTTCAGGAAGAACTGTGTTGTGGGCATTGAAGCTAATCGCAACCATATTGATAATTTGATGCGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC