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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTAGGAACATACTTGGGACCTGAAACCGACGCTGCCGACGACGAATATGTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACACgtgcgtatgtttattttcgagtttgcttttgcagttgctaatgtccatcatgtcctctctttgttatggtggttattgattaaatgaatcgatggaagccagttttaattttgtaaagtattgtcaattttgcagcgaccacctgcatgtgactggtactgataccttctccaattgagcag

Basic information

species Physcomitrella patens
transcript PP1S46_300V6.1
intron # 2
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|100383574|gb|BY950358.1|BY950358
EST:     GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACAC                         TGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
genomic: GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACACgtgcgtatgt ... aattgagcagTGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
EST: gi|100432527|gb|BY960501.1|BY960501
EST:     GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACAC                         TGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
genomic: GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACACgtgcgtatgt ... aattgagcagTGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
EST: gi|100428645|gb|BY959363.1|BY959363
EST:     GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACAC                         TGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
genomic: GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACACgtgcgtatgt ... aattgagcagTGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
EST: gi|100405074|gb|BY991426.1|BY991426
EST:     GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACAC                         TGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
genomic: GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACACgtgcgtatgt ... aattgagcagTGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
EST: gi|100419830|gb|BY957729.1|BY957729
EST:     GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACAC                         TGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
genomic: GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACACgtgcgtatgt ... aattgagcagTGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
EST: gi|100383469|gb|BY950253.1|BY950253
EST:     GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACAC                         TGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT
genomic: GTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACACgtgcgtatgt ... aattgagcagTGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTAT

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: 35 (upstream exon), 18 (downstream exon)
Score: 5

GAGTAGGAACATACTTGGGACCTGAAACCGACGCTGCCGACGACGAATATGTCGAAGCGATGACGAAAGCACTGGCCGTCGGCGTAAATGTACTAGACACgtgcgtatgt ... aattgagcagTGCAGTGAATTACCGTAGTACACGGAGTGAGCGAGCAGTTCGGCGTGCTATCTCTGAAGGTATCAGGTTGGGGTCTATTACGAGGGAGCAGGTAATCGTT




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