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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGAATTGCGAGAGGACTTCAGATTGGCGTGAGTGGACGTCGAAGGTGGTCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAGgtgaggctatgaacattgctgtggcgaaaataagttagggtttcggagtggcttggcgaggttatgaactgtgagcgtatttttgagtcgggttcgtcag...

Basic information

species Physcomitrella patens
transcript PP1S4_73V6.1
intron # 1
splice site 5'
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|67703039|gb|BJ963272.1|BJ963272
EST:     TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAG                         GAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
genomic: TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAGgtgaggctat ... ttgtgcgaagGAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
EST: gi|18355135|gb|BJ187194.1|BJ187194
EST:     TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAG                         GAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
genomic: TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAGgtgaggctat ... ttgtgcgaagGAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
EST: gi|18332448|gb|BJ164461.1|BJ164461
EST:     TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAG                         GAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
genomic: TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAGgtgaggctat ... ttgtgcgaagGAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
EST: gi|100363873|gb|BY966213.1|BY966213
EST:     TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAG                         GAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
genomic: TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAGgtgaggctat ... ttgtgcgaagGAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
EST: gi|67717889|gb|BJ968148.1|BJ968148
EST:     TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAG                         GAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
genomic: TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAGgtgaggctat ... ttgtgcgaagGAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT
EST: gi|67719827|gb|BJ970086.1|BJ970086
EST:     TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAG                         GAATCCGTCTGGAGACGCGAGTATAGGGACAATATTGGAATAGGGTTTGGT
genomic: TCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAGgtgaggctat ... ttgtgcgaagGAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGT

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: 24 (upstream exon), 35 (downstream exon)
Score: 8

CTTGAATTGCGAGAGGACTTCAGATTGGCGTGAGTGGACGTCGAAGGTGGTCACGATCCTTCGAATTCTTCATCGTTTTGCTTCTGCAAGTGATTGTAAGgtgaggctat ... ttgtgcgaagGAATCCGTCTGGAGACGCGAGTATAGGGAGAATATTGGAATAGGGTTTGGTTAGGATGAAGATCGAGGAGGTGCAATCCACTACGAAAAAGCAGAGAGTT




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