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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctgcataacgttggccaaatttcccttcatcactttgctgccactcccattcaccccatttttctacaaagtttgtgggttaagttctgagtttctttctttcttttcttttttttgtgtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG

Basic information

species Physcomitrella patens
transcript PP1S100_191V6.1
intron # 4
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|162164460|gb|FC341573.1|FC341573
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162277582|gb|FC453525.1|FC453525
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162183700|gb|FC359096.1|FC359096
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162245206|gb|FC422135.1|FC422135
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162150325|gb|FC326597.1|FC326597
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162198198|gb|FC372589.1|FC372589
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162166456|gb|FC342438.1|FC342438
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162191940|gb|FC366945.1|FC366945
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162254706|gb|FC430995.1|FC430995
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
EST: gi|162171142|gb|FC347756.1|FC347756
EST:     GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAG                         AATCTGGGACAGGATCTGGCCGCGAGATTGTG
genomic: GTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG

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: 19 (upstream exon), 35 (downstream exon)
Score: 6

GAGGCACTTGACTTACAAAGAAACGCTATGGAGAGAGCTCTCCAGACGAAGTCTATTAAGACTCTAGTGAGATACCCAGAAGACGCAGAGGAGAAATCAGgtcagctgca ... gtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgggttaagttctgagtttctttctttcttttcttttttttgtgtatgtacagAATCTGGGACAGGATCTGGCCGCGAGATTGTG
           ttctgagtttctttct  CT-rich tract
                      tttctttcttttcttt  TA-rich tract