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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattatgcgtatcacagcgaaagccttacagctgtatatagtaatggccaaaggaatgcagacaccatgatactgatttgaatattgaaaatgaggcagGAAATACTTTGTGGATGATGACGATTTTGTTGCGAAGGAT

Basic information

species Physcomitrella patens
transcript PP1S327_30V6.2
intron # 2
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|100396736|gb|BY953801.1|BY953801
EST:     ACATTTCCGAATCCCCTGAAGTTCAACCCAGCGTACTCTGCTGTTAA                         GAAATACTTTGTGGATGATGACGATTTTGTTGCGAAGGAT
genomic: ACATTTCCGAATCCCCTGAAGTTCAACCCAGCGTACTCTGCTGTTAAgtaaggatcg ... aatgaggcagGAAATACTTTGTGGATGATGACGATTTTGTTGCGAAGGAT
EST: gi|67508211|gb|BJ941082.1|BJ941082
EST:     ACATTTCCGAATCCCCTGAAGTTCAACCCAGCGTACTCTGCTGTTAA                         NAAATACTTTGTGGATGATGACGATTTTGTTG
genomic: ACATTTCCGAATCCCCTGAAGTTCAACCCAGCGTACTCTGCTGTTAAgtaaggatcg ... aatgaggcagGAAATACTTTGTGGATGATGACGATTTTGTTG
EST: gi|162261187|gb|FC437204.1|FC437204
EST:     ACATTTCCGAATCCCCTGAAGTTCAACCCAGCGTACTCTGCTGTTAA                         GAAATACCTTGTGGATGATGACGATTTTGTTGCGAAGGAT
genomic: ACATTTCCGAATCCCCTGAAGTTCAACCCAGCGTACTCTGCTGTTAAgtaaggatcg ... aatgaggcagGAAATACTTTGTGGATGATGACGATTTTGTTGCGAAGGAT

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: 18 (upstream exon), 34 (downstream exon)
Score: 6

ACATTTCCGAATCCCCTGAAGTTCAACCCAGCGTACTCTGCTGTTAAgtaaggatcg ... aatgaggcagGAAATACTTTGTGGATGATGACGATTTTGTTGCGAAGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggccaaaggaatgcagacaccatgatactgatttgaatattgaaaatgaggcagGAAATACTTTGTGGATGATGACGATTTTGTTGCGAAGGAT
                          tactgat  putative branch site (score: 6)
                               atttgaatattgaaaa  TA-rich tract