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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattctgtgtatcattcttccttacaggttttcttcaaacagtggaaggatctgaatcttttaacaagtctatggctattttatgtgacag

Basic information

species Physcomitrella patens
transcript PP1S90_28V6.4
intron # 4
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|100355472|gb|BY945951.1|BY945951
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100391837|gb|BY989572.1|BY989572
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGACG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|67573440|gb|BJ946264.1|BJ946264
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|18365163|gb|BJ197237.1|BJ197237
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100377879|gb|BY986439.1|BY986439
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|162278698|gb|FC454808.1|FC454808
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100361319|gb|BY965781.1|BY965781
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|18356191|gb|BJ188250.1|BJ188250
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|208385252|gb|DC915052.1|DC915052
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|208361425|gb|DC935112.1|DC935112
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100386104|gb|BY970043.1|BY970043
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|18331507|gb|BJ163518.1|BJ163518
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100363976|gb|BY966264.1|BY966264
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|208375453|gb|DC936996.1|DC936996
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|162225064|gb|FC401688.1|FC401688
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTAGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100378191|gb|BY949726.1|BY949726
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|18360912|gb|BJ192976.1|BJ192976
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100365162|gb|BY966841.1|BY966841
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|18364385|gb|BJ196458.1|BJ196458
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100448660|gb|CJ972959.1|CJ972959
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100375395|gb|BY948855.1|BY948855
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|18359114|gb|BJ191174.1|BJ191174
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|162237033|gb|FC413192.1|FC413192
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTAGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|18349313|gb|BJ181362.1|BJ181362
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100406861|gb|BY955754.1|BY955754
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100444932|gb|BY982760.1|BY982760
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100388010|gb|BY988483.1|BY988483
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100385258|gb|BY950850.1|BY950850
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|100418007|gb|BY993291.1|BY993291
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|18369448|gb|BJ201535.1|BJ201535
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA
EST: gi|162158960|gb|FC334820.1|FC334820
EST:     GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATG                         CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTAGGGAGTGGAGGAGAGA
genomic: GGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGA

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: 31 (upstream exon), 35 (downstream exon)
Score: 82

GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattc ... tatgtgacagCTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG




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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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGCACCTTATGAGCGGCCTGCTCTGAGCAAAGCTTACTTGTTCCCTGATGgtaaggattctgtgtatcattcttccttacaggttttcttcaaacagtggaaggatctgaatcttttaacaagtctatggctattttatgtgacag

- - - - - - - - - - - - - - GCAAAG