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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcacttggtgtcattgcaaataagatgtctcactgtgtggctctgattctggatttggttttgggaagtctgtattaagtatttgaattgattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTAAACCCACGGAACAAGCCAGGTCGACTCACTGTTATTGTGCGAATGGGAG

Basic information

species Physcomitrella patens
transcript PP1S36_31V6.1
intron # 3
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|162156274|gb|FC332298.1|FC332298
EST:     GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
EST: gi|162219668|gb|FC395664.1|FC395664
EST:     GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
EST: gi|162168089|gb|FC343779.1|FC343779
EST:     GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
EST: gi|162185170|gb|FC362304.1|FC362304
EST:     GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
EST: gi|162248092|gb|FC420097.1|FC420097
EST:     GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
EST: gi|162194172|gb|FC369684.1|FC369684
EST:     GCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
EST: gi|67720594|gb|BJ970853.1|BJ970853
EST:     GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
EST: gi|162176951|gb|FC353628.1|FC353628
EST:     GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
EST: gi|162160220|gb|FC337117.1|FC337117
EST:     GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAG                         GTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA
genomic: GTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTA

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), 21 (downstream exon)
Score: 21

TTGTTCAGCACATTTTGTGTGGATGGGCGAGCGAACCCGGCAGTTAGATGGTGCTCATATTGAATTTCTGCGAGGAGTTGCTAATCCTTTGGGAGTGAAGgtaacccgct ... gattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTAAACCCACGGAACAAGCCAGGTCGACTCACTGTTATTGTGCGAATGGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctggatttggttttgggaagtctgtattaagtatttgaattgattgtgtagGTAAGTGACAAGATGGACCCCGCAGAGTTGGTGAAGCTCTGTGAGATTCTAAACCCACGGAACAAGCCAGGTCGACTCACTGTTATTGTGCGAATGGGAG
                                         aattgat  putative branch site (score: 21)
                            tattaagtatttgaat  TA-rich tract