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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTATAACAAACATGAAAGATGACGAAATTGAAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatcattcgagttcgtttctttatcgaatatctgaatgggtaatgatcgtcttggaggtgtaagtgggagtttccttaacagcttttgatgcttttacag

Basic information

species Physcomitrella patens
transcript PP1S43_166V6.1
intron # 19
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|37852255|gb|BJ610263.1|BJ610263
EST:     AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
EST: gi|162222919|gb|FC399381.1|FC399381
EST:     AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
EST: gi|37842145|gb|BJ600153.1|BJ600153
EST:     ATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: ATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
EST: gi|100390331|gb|BY952739.1|BY952739
EST:     AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
EST: gi|37836849|gb|BJ594857.1|BJ594857
EST:     AAGAGTTAGAGGCAAAAATCTGNCCCGATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
EST: gi|162254784|gb|FC430761.1|FC430761
EST:     ATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: ATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
EST: gi|162255906|gb|FC431982.1|FC431982
EST:     AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
EST: gi|67697565|gb|BJ957798.1|BJ957798
EST:     AGAGTTAGAGGCAAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: AGAGTTAGAGGC-AAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
EST: gi|162255907|gb|FC431983.1|FC431983
EST:     AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAG                         GTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA
genomic: AAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAA

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: 23 (upstream exon), 18 (downstream exon)
Score: 4

GTTATTATAACAAACATGAAAGATGACGAAATTGAAGAGTTAGAGGCAAAAATCTGGCCCGATGCCAGGGAAGGCAGTTATAAGgtaatggatc ... gcttttacagGTACCGTTCTCAAAAGTGTGTTACATAGAGTCTTCTGATTTTCGACTGGAAGACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTA




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