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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatctcataatcaccgcagagaaattctttccaatcaaaccatgtttgaaagagttgttatttgattacagactggagtaacctttaacatttttcgatttggtcaaatggtttctgacttttgagatgatggatgtgacttgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATTCTTTACACCATGTCGTGGCCAGAGCGTATTCCCTGTTCAGAGAAGACAT

Basic information

species Physcomitrella patens
transcript PP1S73_243V6.1
intron # 11
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|16137456|gb|BI894320.1|BI894320
EST:     ATATTGTTGATCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAG                         GACTCCTCACTCATTGCCCAATTAGGCTGGCCAGACATGCCGCTACCCATT
genomic: ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|162244459|gb|FC422632.1|FC422632
EST:     ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|162155914|gb|FC332463.1|FC332463
EST:     ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|67692973|gb|BJ953206.1|BJ953206
EST:     ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|162155913|gb|FC332462.1|FC332462
EST:     ATATTGTTGTTCATCCCCAATCAATTA-TCATTCCAT-GTGGAGACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|162244458|gb|FC422631.1|FC422631
EST:     ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|162171164|gb|FC347778.1|FC347778
EST:     ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: ATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|67694754|gb|BJ954987.1|BJ954987
EST:     CCAATCCATTATTCATTCCATGGGGGAGACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: CCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|208348677|gb|DC926352.1|DC926352
EST:     TTATTCATTCCATGGTGGAGACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: TTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
EST: gi|162204514|gb|FC381937.1|FC381937
EST:     GTGG-GACGCAG                         GACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT
genomic: GTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATT

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), 32 (downstream exon)
Score: 12

GGAAGTGATTGAAGCCCATTATCTCTTCGGAGCTGATTACGATGATATTGATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtttatctca ... tgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATTCTTTACACCATGTCGTGGCCAGAGCGTATTCCCTGTTCAGAGAAGACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttggtcaaatggtttctgacttttgagatgatggatgtgacttgtctgatagGACTCCTCAGTCATTGCCCAATTAGGCTGGCCAGACATGCGGCTACCCATTCTTTACACCATGTCGTGGCCAGAGCGTATTCCCTGTTCAGAGAAGACAT
                ttctgac  putative branch site (score: 12)
                                           cttgtct  putative PPT