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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacctaaaagttatgtagagttcatttgtaatattttttaaaacagttgttttaaggctacattatcttagtatgtggttatgggtgtctgtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCGCTTAAGAATCCCGAAAG

Basic information

species Physcomitrella patens
transcript PP1S41_177V6.1
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|162192525|gb|FC368635.1|FC368635
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|18345999|gb|BJ178042.1|BJ178042
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCA
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCA
EST: gi|162230102|gb|FC406250.1|FC406250
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|18344702|gb|BJ176743.1|BJ176743
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|208350063|gb|DC910298.1|DC910298
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|162263739|gb|FC439638.1|FC439638
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|100353603|gb|BY964889.1|BY964889
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|208354187|gb|DC902443.1|DC902443
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|162249310|gb|FC423980.1|FC423980
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|100389012|gb|BY952216.1|BY952216
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
EST: gi|67569370|gb|BJ942194.1|BJ942194
EST:     ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCG                         CCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG
genomic: ATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCG

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: 16 (upstream exon), 31 (downstream exon)
Score: 3

AGGAAAGTGGGAGCAGACTTCCAAATCAATTGAATTGCTGGACCCTCTGAATGGGGAAAAATTCATATCTGTTCCCGATACCTCTATCGATGAAATATCGgtgtgcactc ... gtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCGCTTAAGAATCCCGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttttaaggctacattatcttagtatgtggttatgggtgtctgtcatgacagCCATTTGTACAAAGCTTACGGGCATGCTCAAAGTCAGGTCTGCACAACCCGCTTAAGAATCCCGAAAG
                attatctta  TA-rich tract