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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTTCACAATATATGCAACGTTACCCATCTTTCAAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctcataccatagtgatctctcttttattcgtttgcaagtggaggttttggaattgatacacagtttgatcattacaccatcatatttcaggtat...

Basic information

species Physcomitrella patens
transcript PP1S91_64V6.3
intron # 16
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|208385728|gb|DC952889.1|DC952889
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|37828196|gb|BJ586208.1|BJ586208
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|208373036|gb|DC948801.1|DC948801
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|162197940|gb|FC373669.1|FC373669
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|37822942|gb|BJ581008.1|BJ581008
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|37830159|gb|BJ588171.1|BJ588171
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|162196323|gb|FC374366.1|FC374366
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|37837195|gb|BJ595203.1|BJ595203
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGCGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|37824436|gb|BJ582502.1|BJ582502
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|37845572|gb|BJ603580.1|BJ603580
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|162196322|gb|FC374365.1|FC374365
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
EST: gi|37827243|gb|BJ585255.1|BJ585255
EST:     AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACG                         ACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT
genomic: AAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTT

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: 33 (upstream exon), 34 (downstream exon)
Score: 5

GATGTTCACAATATATGCAACGTTACCCATCTTTCAAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctca ... cctttgacagACCTATGACTGCAACAATGGAGGAGGTGACAAGAAACCCTTCGCTACAGTTGTTGCTAACGAGCATATATACCTCTTGAAAATTCTTTCGAGACGGTAGG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTTCACAATATATGCAACGTTACCCATCTTTCAAAAATATGATCAAAGATTCAGCTTGGCTACAACGCTTTTTGGGGAAACGgtaattctcataccatagtgatctctcttttattcgtttgcaagtggaggttttggaattgatacacagtttgatcattacaccatcatatttcaggtat

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