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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgttgtttgaatgagttttgagggttccatcgccatgtgggttaccgtgcttttctgtggttgaggaacacagagtgctgttgttgtgtaagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAAAGTCTACGGCATTGCTACTTACAACTGTCAGAGAGTGACCTTGGCTCTC

Basic information

species Physcomitrella patens
transcript PP1S46_325V6.1
intron # 1
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|100387711|gb|BY951711.1|BY951711
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|18349970|gb|BJ182021.1|BJ182021
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|18356177|gb|BJ188236.1|BJ188236
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|18348858|gb|BJ180907.1|BJ180907
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|208387810|gb|DC941379.1|DC941379
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|208393393|gb|DC942491.1|DC942491
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|208379946|gb|DC927672.1|DC927672
EST:     GCAGCGCATCCCAGACCAATACCAACNTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: GCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|18346616|gb|BJ178661.1|BJ178661
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|208353247|gb|DC913921.1|DC913921
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|162269339|gb|FC444817.1|FC444817
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|18353097|gb|BJ185152.1|BJ185152
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|15327526|gb|BI488280.1|BI488280
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
EST: gi|208344704|gb|DC905153.1|DC905153
EST:     TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAG                         ACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA
genomic: TGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 14

TAGTCACGATGAGTTTGATCGTGTTGTTGTTGCAGCTGATTGAATGTTTTTGTCTGTGCAGCGCATCCCAGACCAATACCAACTTTGAGGCTTGTGCGAGgtctgtaact ... taagccacagACTGGTGCAACAAGGCGAAGGATTCAAAGGACGTGGAGCTATGGGAATCAAAGTCTACGGCATTGCTACTTACAACTGTCAGAGAGTGACCTTGGCTCTC




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