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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatacagaaccagcaacttagtgatagtattgtaggatgatttagtacaatgggtcgttgttttccgttttgagactgaaatagagatttgttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGAAG

Basic information

species Physcomitrella patens
transcript PP1S99_201V6.1
intron # 6
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|162151171|gb|FC327157.1|FC327157
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162221878|gb|FC398445.1|FC398445
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162167067|gb|FC342529.1|FC342529
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162226649|gb|FC402733.1|FC402733
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|208386153|gb|DC949064.1|DC949064
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162190768|gb|FC367030.1|FC367030
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|208361835|gb|DC950107.1|DC950107
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162229328|gb|FC405519.1|FC405519
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|67695217|gb|BJ955450.1|BJ955450
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162190767|gb|FC367029.1|FC367029
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162226648|gb|FC402732.1|FC402732
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162202685|gb|FC379004.1|FC379004
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162202684|gb|FC379003.1|FC379003
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
EST: gi|162229329|gb|FC405520.1|FC405520
EST:     AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG                         ATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA
genomic: AGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGA

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: 49

GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAGgtaatgattt ... gttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaatgggtcgttgttttccgttttgagactgaaatagagatttgttcgttcagATTGATGTGGATGTGGCCACTCATGTTACTGTTACAAGGGAAGGTTCTCGAAG
                                          tttgttc  CT-rich tract
            ttgtttt  TA-rich tract