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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacaaatcaacttatctctgtattgataaaatctaattcatgtacgaactccagaagatcttcaatgtcaggaggctggtattcttgtttatactaagccttgaaatgtatttttttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGATTTGCTAATCGGCAGTTTGGTGTAGCAGTGAGATTGTTACGCAATCTTG

Basic information

species Physcomitrella patens
transcript PP1S93_148V6.1
intron # 4
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|162180967|gb|FC358621.1|FC358621
EST:     TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAG                         GTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
genomic: TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAGgtacacaaat ... ttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
EST: gi|162156828|gb|FC333640.1|FC333640
EST:     TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAG                         GTACCAGATTGGTCCCATNCA-GTGACCACTGCAGT
genomic: TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAGgtacacaaat ... ttttgagtagGTACCAGATTGGTCCCAT-CAAGTGACCACTGCAGT
EST: gi|100389857|gb|BY971209.1|BY971209
EST:     TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAG                         GTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
genomic: TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAGgtacacaaat ... ttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
EST: gi|162254310|gb|FC430445.1|FC430445
EST:     TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAG                         GTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
genomic: TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAGgtacacaaat ... ttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
EST: gi|37822501|gb|BJ580567.1|BJ580567
EST:     TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAG                         GTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
genomic: TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAGgtacacaaat ... ttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
EST: gi|162254309|gb|FC430444.1|FC430444
EST:     TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAG                         GTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
genomic: TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAGgtacacaaat ... ttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
EST: gi|162270470|gb|FC447586.1|FC447586
EST:     TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAG                         GTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA
genomic: TGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAGgtacacaaat ... ttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGA

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: 15 (upstream exon), 35 (downstream exon)
Score: 3

AGAGATGTTCATCTATGTGGATGCTGCAAATAGTGAAGCATTGCAAGAAATGCTTGCTGCAGTGCACAAACGTATGTCTAATGCTGTTGCTAGTCTTGAGgtacacaaat ... ttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGATTTGCTAATCGGCAGTTTGGTGTAGCAGTGAGATTGTTACGCAATCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaggctggtattcttgtttatactaagccttgaaatgtatttttttttgagtagGTACCAGATTGGTCCCATCAAGTGACCACTGCAGTCCCGGGAGCCTTGCGATTTGCTAATCGGCAGTTTGGTGTAGCAGTGAGATTGTTACGCAATCTTG
                                      tattttttttt  CT-rich tract
                              ttgaaatgtatttttt  TA-rich tract