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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatgtgtcttggagactgagcttccttactgacccacagtttcagtatcatgtgttcttggacttatctaattctcttttttctctgcatcatccagCTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAG

Basic information

species Physcomitrella patens
transcript PP1S90_13V6.1
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|22132775|gb|BQ827349.1|BQ827349
EST:     GGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCG                         CTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
genomic: GGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCGgtaaaatatc ... catcatccagCTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
EST: gi|162190182|gb|FC365924.1|FC365924
EST:     AGGATCATCCCGGGGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCG                         CTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
genomic: AGGATCATCCCGGGGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCGgtaaaatatc ... catcatccagCTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
EST: gi|162162473|gb|FC339204.1|FC339204
EST:     AGGATCATCCCGGGGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCG                         CTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
genomic: AGGATCATCCCGGGGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCGgtaaaatatc ... catcatccagCTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
EST: gi|162186442|gb|FC362998.1|FC362998
EST:     AGGATCATCCCGGGGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCG                         CTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
genomic: AGGATCATCCCGGGGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCGgtaaaatatc ... catcatccagCTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
EST: gi|22132757|gb|BQ827332.1|BQ827332
EST:     GAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCG                         CTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT
genomic: GAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCGgtaaaatatc ... catcatccagCTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCT

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: 33 (upstream exon), 35 (downstream exon)
Score: 26

GTGGGTTTTAGATGCTACACCTGGCAAGGTTCGATCTGGTGGAGATGGTGAGGATCATCCCGGGGAACTGATTGCAACTCTTCGCAAGATGCCAGCCTCGgtaaaatatc ... catcatccagCTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtatcatgtgttcttggacttatctaattctcttttttctctgcatcatccagCTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAG
                       atctaat  putative branch site (score: 26)
                             ttctcttttttctctg  CT-rich tract
                          taattctctttttt  TA-rich tract