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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttcaagttcgttctagtatttcttccaacaactactgttgggtaatcgattcctctaaattggctcacaatttcttgcgtctcttattcatgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAATGCCTGGGAGTCTTTGGACTCGGAGTCGGAACGTGTTGATGAATACAGTC

Basic information

species Physcomitrella patens
transcript PP1S276_96V6.1
intron # 16
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|162184902|gb|FC361412.1|FC361412
EST:     ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAG                         ATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
genomic: ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
EST: gi|162177777|gb|FC354611.1|FC354611
EST:     ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAG                         ATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
genomic: ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
EST: gi|162178338|gb|FC355160.1|FC355160
EST:     ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAG                         ATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
genomic: ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
EST: gi|162177778|gb|FC354612.1|FC354612
EST:     ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAG                         ATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
genomic: ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
EST: gi|100373379|gb|BY949300.1|BY949300
EST:     ATGCAGATGATACCGGGTACGAAGATGAGTACCNACTAGAAGATTTGGAG                         ATTACAGCACCTGACTACATCCTGAANGGAAG-AGTGTCAAACTTCAGAAA
genomic: ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAA-GGAAGGAGTGTCAAACTTCAGAAA
EST: gi|162178337|gb|FC355159.1|FC355159
EST:     ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAG                         ATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
genomic: ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
EST: gi|100366973|gb|BY948304.1|BY948304
EST:     ATGCAGATGATACCGGGTACGAAGATGAGTACCNACTAGAAGATTTGGAG                         ATTACAGCACCTGACTACATCCTGAANGAAGGAGTGTCNAACTTCAGAAAT
genomic: ATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT
EST: gi|18338550|gb|BJ170574.1|BJ170574
EST:     AGATGAGTACCAACTAGAAGATTTGGAG                         ATTACAGCACCTGACTACATCNTGAAGGAAGGAGTGTCAAACTTCAGAAAT
genomic: AGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAAT

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), 35 (downstream exon)
Score: 23

GTGGATCCCAGTACAGGTGATGCAGATGATACCGGGTACGAAGATGAGTACCAACTAGAAGATTTGGAGgtgggatttc ... catgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAATGCCTGGGAGTCTTTGGACTCGGAGTCGGAACGTGTTGATGAATACAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcgattcctctaaattggctcacaatttcttgcgtctcttattcatgcaccagATTACAGCACCTGACTACATCCTGAAGGAAGGAGTGTCAAACTTCAGAAATGCCTGGGAGTCTTTGGACTCGGAGTCGGAACGTGTTGATGAATACAGTC
                  ggctcac  putative branch site (score: 23)
                                    tctcttattc  putative PPT
          tctaaatt  TA-rich tract