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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttttcacctatattattgtgtgctttattctgggacataatgatgtatgcatgtatctacaaatgtatggcattcctatcgtgctgtatcgtctatatagatccttgctgtaagcctaatgactgacatatgtttttattttaaaaattttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCATCTTGGTATTG

Basic information

species Physcomitrella patens
transcript PP1S430_12V6.1
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|162172856|gb|FC348861.1|FC348861
EST:     CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAG                         AGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
genomic: CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAGgtgatttttc ... tttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
EST: gi|100440623|gb|BY962310.1|BY962310
EST:     CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAG                         AGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
genomic: CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAGgtgatttttc ... tttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
EST: gi|162159612|gb|FC335790.1|FC335790
EST:     CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAG                         AGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
genomic: CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAGgtgatttttc ... tttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
EST: gi|162199548|gb|FC373200.1|FC373200
EST:     CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAG                         AGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
genomic: CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAGgtgatttttc ... tttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
EST: gi|162240779|gb|FC416345.1|FC416345
EST:     CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAG                         AGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
genomic: CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAGgtgatttttc ... tttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
EST: gi|162257199|gb|FC433075.1|FC433075
EST:     CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAG                         AGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA
genomic: CTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAGgtgatttttc ... tttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCA

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: 35 (upstream exon), 34 (downstream exon)
Score: 11

GTTTACATTATTGATTTCGGTCTTGCAAAGAAGTATCGCGATCCCTCCACTCACCAGCACATACCTTACAGgtgatttttc ... tttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCATCTTGGTATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgctgtaagcctaatgactgacatatgtttttattttaaaaattttcttttagAGAAAATAAAAACCTCACTGGGACTGCACGATATGCCAGCATCAACACCCATCTTGGTATTG
                 gactgac  putative branch site (score: 11)
                                            ttttctttt  putative PPT
                  actgacatatgttttt  TA-rich tract