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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcacacatccgatttcgtttgttgaatgctcttcaccacgccctaatctatccttagtcaggatatgctgcctcgagtcttgtcttgcttgctgatgtctaagaacgcatgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTCTGTGCCTCTGTTGCCGACACCGCTGGGGAACGCATTTGGGTGGCAAGGC

Basic information

species Physcomitrella patens
transcript PP1S80_41V6.1
intron # 9
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|162262833|gb|FC439993.1|FC439993
EST:     AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAG                         TTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
genomic: AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAGgtcacacatc ... atgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
EST: gi|162186700|gb|FC362736.1|FC362736
EST:     AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAG                         TTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
genomic: AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAGgtcacacatc ... atgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
EST: gi|67724729|gb|BJ974988.1|BJ974988
EST:     AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAG                         TTATGGCGATTGACACTTGACGGGGAATTTCGGAACGATTACACTGGTTTC
genomic: AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAGgtcacacatc ... atgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
EST: gi|162262832|gb|FC439992.1|FC439992
EST:     AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAG                         TTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
genomic: AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAGgtcacacatc ... atgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
EST: gi|208379427|gb|DC922971.1|DC922971
EST:     AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAG                         TTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
genomic: AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAGgtcacacatc ... atgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC
EST: gi|67723823|gb|BJ974082.1|BJ974082
EST:     AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAG                         TTATGGCGATTGACACTCGACGGGGAACTTCGGAACGATTACACTGGTTTC
genomic: AAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAGgtcacacatc ... atgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTC

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: 32 (upstream exon), 27 (downstream exon)
Score: 6

TGGATGTCTTGCTGCTGACGTCCTTGGAATTCCGAACAGCGACGTGCAGCAAGCAAGGATGTCTGAGAGTGCAGGATGTAGTCGTGGAGAACCAAATCAGgtcacacatc ... atgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTCTGTGCCTCTGTTGCCGACACCGCTGGGGAACGCATTTGGGTGGCAAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctgcctcgagtcttgtcttgcttgctgatgtctaagaacgcatgtgcacagTTATGGCGATTGACACTTGACGGGGAACTTCGGAACGATTACACTGGTTTCTGTGCCTCTGTTGCCGACACCGCTGGGGAACGCATTTGGGTGGCAAGGC
                          tgctgat  putative branch site (score: 6)