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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcaggattttcatattggatatgatcgaggttttatttcgagatttcctgattttttcgttgtgggatacaataagtcttaagtatattgtccaaaccgtcttgcatcagcgaccgtctagtttcatctgacaatatagttggtatctaaatctacag

Basic information

species Physcomitrella patens
transcript PP1S4_215V6.1
intron # 3
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|22491814|gb|BU051737.1|BU051737
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACTTAGACCGAATGTCATACCAG                         GATAGATTTAAGGCCTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|162264332|gb|FC440498.1|FC440498
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|18333863|gb|BJ165879.1|BJ165879
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|18332708|gb|BJ164721.1|BJ164721
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|162238939|gb|FC417703.1|FC417703
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|208371352|gb|DC944516.1|DC944516
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|100357608|gb|BY946481.1|BY946481
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAGGCATCAGGGGTTC
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTC
EST: gi|162199675|gb|FC375914.1|FC375914
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|67696462|gb|BJ956695.1|BJ956695
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|162238938|gb|FC417702.1|FC417702
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|162179827|gb|FC356418.1|FC356418
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|162264333|gb|FC440499.1|FC440499
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|162235909|gb|FC411652.1|FC411652
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
EST: gi|162199674|gb|FC375913.1|FC375913
EST:     ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAG                         GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG
genomic: ACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTG

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: 28 (upstream exon), 34 (downstream exon)
Score: 20

TCCAATCCGGTCGTTGTTGGAGGCAGGATTTGATGCCCATAAACGAAAAGACGTGCGTCTATATTATGGTGCTCGCAACCTAGACCGAATGTCATACCAGgtattctcag ... aaatctacagGATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG




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