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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCTCGACATTGTCGCCGAAAATCCGAATAAATTCAAGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctttacatctgaatacactcctaggctggtatttatgcccttaacatattactaaatgctgttttcttttcaagaatttcagacttggttgca...

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.2
intron # 5
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|18345934|gb|BJ177977.1|BJ177977
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|162156416|gb|FC332648.1|FC332648
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|162168654|gb|FC343916.1|FC343916
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|162179792|gb|FC356383.1|FC356383
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|18329065|gb|BJ161071.1|BJ161071
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|18358713|gb|BJ190772.1|BJ190772
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAG
EST: gi|100375682|gb|BY968157.1|BY968157
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|18358530|gb|BJ190589.1|BJ190589
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|18343769|gb|BJ175807.1|BJ175807
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|18371305|gb|BJ202907.1|BJ202907
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|162250938|gb|FC425760.1|FC425760
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|18326677|gb|BJ158676.1|BJ158676
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGA
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGA
EST: gi|18346948|gb|BJ178993.1|BJ178993
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCT
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCT
EST: gi|208352746|gb|DC905880.1|DC905880
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|100442899|gb|BY963394.1|BY963394
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|162272851|gb|FC448007.1|FC448007
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|162208298|gb|FC384402.1|FC384402
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|100379666|gb|BY949883.1|BY949883
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|18347535|gb|BJ179582.1|BJ179582
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCCTCGTGGCAGTTAAGAACGCTTCATCAGT
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCC-TCGTGGCAGTTAAGAACGCTTCATCAGT
EST: gi|162163958|gb|FC339868.1|FC339868
EST:     GTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: GTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
EST: gi|18363878|gb|BJ195950.1|BJ195950
EST:     AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAG                         ATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG
genomic: AGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTG

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: 39

ACCCTCGACATTGTCGCCGAAAATCCGAATAAATTCAAGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctt ... tctgtttcagATTAAGGCGTTCAGACCTAGCCTCGTGGCAGTTAAGAACGCTTCATCAGTGCCTGCTTTAAAGGAAGCCCTTGCTGGATTGGACAAGCTCCCAGAAATCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCCTCGACATTGTCGCCGAAAATCCGAATAAATTCAAGGTCGTGGCTTTGGCTGCTGGTTCCAATGTCAGCTTGTTGGCTGAACAGgtaatttctttacatctgaatacactcctaggctggtatttatgcccttaacatattactaaatgctgttttcttttcaagaatttcagacttggttgca

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT