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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttagatttctactacctgtcttttgatgtagaacagaactatactctattcgttctgcgagcattgttatccacgaaaatcagctgtcaacgtgccatatggttcatttcattcatgactaggtgtcatctttttcctttttccttttttaactatgagtgatgtgaatttgtag

Basic information

species Physcomitrella patens
transcript PP1S62_200V6.1
intron # 2
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|208381799|gb|DC903297.1|DC903297
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100451406|gb|CJ974750.1|CJ974750
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100420949|gb|BY993540.1|BY993540
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|208377043|gb|DC910831.1|DC910831
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|6102408|gb|AW126878.1|AW126878
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100389005|gb|BY952209.1|BY952209
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCCACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|208346777|gb|DC901547.1|DC901547
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|208393171|gb|DC907994.1|DC907994
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100370792|gb|BY948518.1|BY948518
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100420575|gb|BY976076.1|BY976076
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|208370830|gb|DC936206.1|DC936206
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100370268|gb|BY985326.1|BY985326
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100386901|gb|BY988170.1|BY988170
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|208388769|gb|DC941778.1|DC941778
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100439952|gb|BY980321.1|BY980321
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|18328108|gb|BJ160112.1|BJ160112
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
EST: gi|100409252|gb|BY991921.1|BY991921
EST:     GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAG                         CTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC
genomic: GGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATAC

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: 19

GTGGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttaga ... gaatttgtagCTGCGTCTACTGCACTACTTCCCGACGACAACGCTGTGAAAAGTTTGATACAAAGCTTGTACGATCCATTGTTCGTAATTGGGGCGGGGGGGCTTGGTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTGCTGTACAGAGCAGGCTTAGTGACAGCGGCCACAACATTCGTAGCAGgtagcttagatttctactacctgtcttttgatgtagaacagaactatactctattcgttctgcgagcattgttatccacgaaaatcagctgtcaacgtgccatatggttcatttcattcatgactaggtgtcatctttttcctttttccttttttaactatgagtgatgtgaatttgtag

- - - - - - AGAGCA
- - - - - -  GAGCAG