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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTATGGGCTTCTCTGTGTCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatatttcttattaaaacttgtatgtcgcagttccagctatgtcgcagtttcagatttcttaaatcgtgtaattttgctcttgcaacatgcag

Basic information

species Physcomitrella patens
transcript PP1S98_233V6.1
intron # 4
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|67698313|gb|BJ958546.1|BJ958546
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
EST: gi|18339190|gb|BJ171217.1|BJ171217
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
EST: gi|162207047|gb|FC382161.1|FC382161
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
EST: gi|162208289|gb|FC384393.1|FC384393
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
EST: gi|162207048|gb|FC382162.1|FC382162
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
EST: gi|162238515|gb|FC417396.1|FC417396
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
EST: gi|67574887|gb|BJ947711.1|BJ947711
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
EST: gi|162208290|gb|FC384394.1|FC384394
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
EST: gi|162238514|gb|FC417395.1|FC417395
EST:     TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAG                         GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT
genomic: TCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT

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), 35 (downstream exon)
Score: 35

GGCTATGGGCTTCTCTGTGTCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatattt ... caacatgcagGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTATGGGCTTCTCTGTGTCGGCTACCCTCTGTCAGATATCGAAGTTGAAACTCAGGACGAAGACGAGgtaaatatttcttattaaaacttgtatgtcgcagttccagctatgtcgcagtttcagatttcttaaatcgtgtaattttgctcttgcaacatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA