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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgacttttatacatcttcgattaaatcagcaatctatgtaactgagacgacagctgttttgagtttgagatggaggagcttttgttattgatgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAGAACTTTGGCATTGTTGGAACTGGCCGCCAGCATATAATTGAT

Basic information

species Physcomitrella patens
transcript PP1S392_16V6.1
intron # 1
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|18329681|gb|BJ161687.1|BJ161687
EST:     AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCT                         GTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
genomic: AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCTgtaagccttg ... atgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
EST: gi|208361429|gb|DC935116.1|DC935116
EST:     AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCT                         GTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
genomic: AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCTgtaagccttg ... atgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
EST: gi|208391744|gb|DC942306.1|DC942306
EST:     AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCT                         GTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
genomic: AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCTgtaagccttg ... atgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
EST: gi|18362764|gb|BJ194835.1|BJ194835
EST:     AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCT                         GTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
genomic: AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCTgtaagccttg ... atgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
EST: gi|100356264|gb|BY946277.1|BY946277
EST:     AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCT                         GTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
genomic: AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCTgtaagccttg ... atgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
EST: gi|100373887|gb|BY967842.1|BY967842
EST:     AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCT                         GTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
genomic: AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCTgtaagccttg ... atgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
EST: gi|100405482|gb|BY955547.1|BY955547
EST:     AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCT                         GTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG
genomic: AGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCTgtaagccttg ... atgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAG

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: 7

AACAAGCAGGAAGGAAGGACTGTGGCGCCTCTGGAGCTCCTAGGATTGGAAGAGCGTCGTCAGGATGCCAGTGTTTAAGACGGCCTTCAATGGATACTCTgtaagccttg ... atgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAGAACTTTGGCATTGTTGGAACTGGCCGCCAGCATATAATTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgacagctgttttgagtttgagatggaggagcttttgttattgatgtttgcagGTAAAGTTTAGCCCTTTTCTGGAGAATCGCCTAGCTGTATCCACTTCAGAGAACTTTGGCATTGTTGGAACTGGCCGCCAGCATATAATTGAT
                                        tattgat  putative branch site (score: 7)
                                  ttttgttatt  TA-rich tract