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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGCAATCGGCGTTCTTAAGGGAGGCTTCGAAATTTATGGGTGTGAAGTATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtcgcccgagtgaaactgatatgtgtttcttcttcactgtgtttagttcgattttttgcttttgttttcgtggagcttgacactcaggtgccccttgttggatattactcttctcggatcgtacatctgatggttctctcttggtgtttgggtgtttgtttccttccttgtttacag

Basic information

species Physcomitrella patens
transcript PP1S97_54V6.4
intron # 1
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|37841964|gb|BJ599972.1|BJ599972
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|18332442|gb|BJ164455.1|BJ164455
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|208388641|gb|DC953431.1|DC953431
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|67696509|gb|BJ956742.1|BJ956742
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|37835663|gb|BJ593675.1|BJ593675
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|18337853|gb|BJ169877.1|BJ169877
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|162249476|gb|FC426746.1|FC426746
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|18338064|gb|BJ170088.1|BJ170088
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|67574156|gb|BJ946980.1|BJ946980
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|162248874|gb|FC422881.1|FC422881
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|18341780|gb|BJ173815.1|BJ173815
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|37850242|gb|BJ608250.1|BJ608250
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|18364771|gb|BJ196844.1|BJ196844
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|37845267|gb|BJ603275.1|BJ603275
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|37853392|gb|BJ611400.1|BJ611400
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|18354273|gb|BJ186329.1|BJ186329
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|67697554|gb|BJ957787.1|BJ957787
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|18347001|gb|BJ179047.1|BJ179047
EST:     TGTTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|162258316|gb|FC434243.1|FC434243
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|162210551|gb|FC386847.1|FC386847
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|37835745|gb|BJ593757.1|BJ593757
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|162224213|gb|FC399277.1|FC399277
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|208368661|gb|DC947936.1|DC947936
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|162258317|gb|FC434244.1|FC434244
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|18354193|gb|BJ186249.1|BJ186249
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|67692998|gb|BJ953231.1|BJ953231
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|67573124|gb|BJ945948.1|BJ945948
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|162249477|gb|FC426747.1|FC426747
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|67569732|gb|BJ942556.1|BJ942556
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|162210550|gb|FC386846.1|FC386846
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
EST: gi|67508263|gb|BJ941132.1|BJ941132
EST:     TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAG                         ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG
genomic: TATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 63

GTCTGCAATCGGCGTTCTTAAGGGAGGCTTCGAAATTTATGGGTGTGAAGTATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtc ... ttgtttacagACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGCAATCGGCGTTCTTAAGGGAGGCTTCGAAATTTATGGGTGTGAAGTATTTCGACTTATTCGACGCTAGTGCCGAAGCATGGATAATTTGGGGCAGgtgaaatgtcgcccgagtgaaactgatatgtgtttcttcttcactgtgtttagttcgattttttgcttttgttttcgtggagcttgacactcaggtgccccttgttggatattactcttctcggatcgtacatctgatggttctctcttggtgtttgggtgtttgtttccttccttgtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA