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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCCTTGATCAGTTTGTGTTTGCATTTTTTTGCCTCAACGTTTCACTCCAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGgtaatttaatgctatttgagctcttatatcgcttcggagagtcacttgcgatgctctagaaaaatcagctgctgcgcagttttcggtcctgtgttttgct...

Basic information

species Physcomitrella patens
transcript PP1S197_22V6.2
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|208359340|gb|DC939107.1|DC939107
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAG                         GGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGgtaatttaat ... tgcagtgtagGGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
EST: gi|100443206|gb|BY981832.1|BY981832
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|208393290|gb|DC942444.1|DC942444
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|100367799|gb|BY984789.1|BY984789
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAG                         GGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGgtaatttaat ... tgcagtgtagGGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
EST: gi|208392219|gb|DC929480.1|DC929480
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|162168953|gb|FC345635.1|FC345635
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|208358314|gb|DC934535.1|DC934535
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|208366765|gb|DC940079.1|DC940079
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|100384610|gb|BY950600.1|BY950600
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAG                         GGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGgtaatttaat ... tgcagtgtagGGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
EST: gi|67717117|gb|BJ967376.1|BJ967376
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|100442468|gb|BY963162.1|BY963162
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAG                         GGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGgtaatttaat ... tgcagtgtagGGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
EST: gi|162186319|gb|FC361627.1|FC361627
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAG                         GGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGgtaatttaat ... tgcagtgtagGGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
EST: gi|208358782|gb|DC942948.1|DC942948
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|100446728|gb|CJ971027.1|CJ971027
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|100434760|gb|BY960826.1|BY960826
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|208346662|gb|DC913308.1|DC913308
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGTGTAG                     
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCT--G-G-G-AGgtaatttaat ... tgcagt
EST: gi|208388708|gb|DC941521.1|DC941521
EST:     CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAG                         GGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA
genomic: CAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGgtaatttaat ... tgcagtgtagGGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAA

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: 34 (upstream exon), 27 (downstream exon)
Score: 3

TGGTCCTTGATCAGTTTGTGTTTGCATTTTTTTGCCTCAACGTTTCACTCCAGGTTGTTCATTGTCTCTGTTAGGGCACGTGACGTTATCTGTCTGGGAGgtaatttaat ... tgcagtgtagGGCTCTGCACAGGCTTTTCTTCGAAGTTTGAGGATATCACTGAGAACAGAAAGTTTCAAAGATGTCGATGGTTTTCGCTCCTCGCATGGCTGAAGCCGCA




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