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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctggctgttaaggttaatcatatctctaactgcatacttactagtcaatgcgcatcagctgatgagcatttctaactatgtttcatcaaaatatgtccatgttgccttagtgttatgttaatgccttgtcaggagtgagtattaaagtggtttctgtttcttgcttgaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTTAACTCTACTCGCCTAGTTGTTAAACCTGATATGTTATTTGGCAAGCGCG

Basic information

species Physcomitrella patens
transcript PP1S63_54V6.2
intron # 2
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|67574237|gb|BJ947061.1|BJ947061
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|208363504|gb|DC935269.1|DC935269
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|100356137|gb|BY946215.1|BY946215
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|100401167|gb|BY990864.1|BY990864
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|18330798|gb|BJ162804.1|BJ162804
EST:     CACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: CACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|18328338|gb|BJ160342.1|BJ160342
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|208376362|gb|DC932272.1|DC932272
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|162235868|gb|FC412419.1|FC412419
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|18346689|gb|BJ178734.1|BJ178734
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|162219070|gb|FC394653.1|FC394653
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|100426836|gb|BY977387.1|BY977387
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
EST: gi|100402496|gb|BY954865.1|BY954865
EST:     AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAG                         GTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT
genomic: AGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTT

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), 23 (downstream exon)
Score: 14

CATGGCAAGGAAGAAGATCAGAGAGTATAACTCAAAACGCATCTTCAAGGAGCACTTGAAGAGGCTAGCAGGCATTGATGTTGATATCAAGGCTGCGCAGgtatgttctg ... gaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTTAACTCTACTCGCCTAGTTGTTAAACCTGATATGTTATTTGGCAAGCGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccttgtcaggagtgagtattaaagtggtttctgtttcttgcttgaaaatccagGTAACACAATCAACAGATTTCAACGAGTTGGCAAACAAGGAAGCATGGCTTAACTCTACTCGCCTAGTTGTTAAACCTGATATGTTATTTGGCAAGCGCG
                agtattaaa  TA-rich tract