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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtacttgacagtgtatcttttgctaatcggtggagttctctcgttgttgtaggttgcgactgtatactgaggtgttcttttggtttctaccaggca...

Basic information

species Physcomitrella patens
transcript PP1S101_184V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_184V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA20G01220.1 (Glycine max), 5'ss of exon 4
GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtacttga---cagtgtatcttttgctaatcggtg--------gagttctctcgttgttgtaggttgcgactgtatactgagg---------tgttcttttggtttctaccaggca-----
|| |||||  |  || |  || | ||||||||  | || ||  | ||||| ||||||||||||||| | ||||||||||| ||||||||   | |||        ||  | || |  | | | | |        |||    || | |   |||  |      |  || || |           | ||| || | |||    |  |       
GACTTGCCAGATTTGATTTCAATAAAGGATGCAAACTTTTCTGATGTGGATGCTGTATTCTGTTGTTTGCCTCATGGAACTACTCAGgttctttcttatgtcttttgagttttgtatttacccgagtttgccaagagagtgcttgataaagtatatcaaatatcaatgcttaaaagttaagactattccttagattttcgtcttgtttccag

upper sequence: PP1S101_184V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA07G29630.1 (Glycine max), 5'ss of exon 5
GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgt--------gtgtacttgacagtgtatcttttgctaa--tcggtg-gagttctctcgttgttgtaggttgcgactgtatactgagg-----------tgttcttttggtttctaccaggca-----
|| |||||  |  || | ||| | ||||||||  | || ||  | ||||| ||||||||||||||| | ||||||||||| ||||||||         |||  ||     | | | |||  || |  | |    |||  | || |||   |||         |  || || |             | ||| || | |||  | |  |       
GACTTGCCAGATTTGATTGCAATAAAGGATGCAAACTTTTCTGATGTGGATGCTGTATTCTGTTGTTTGCCTCATGGAACTACTCAGgttctttcttatgtcttttgagttttgtatttccctgagtttgccaagagagcactggttaaagtataccaaatatcaatgcttaaaagttacaagactattccttagattttcatcttgtttccag
















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|162261824|gb|FC438348.1|FC438348
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|162265711|gb|FC443117.1|FC443117
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|100427283|gb|BY959068.1|BY959068
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGGTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|100365102|gb|BY966811.1|BY966811
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGGTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|100383898|gb|BY987155.1|BY987155
EST:     TCTCACAGGTGGACGCTGTATTCTGTTGTCTTCTTCATGGGACAACTCAG                         GAGATAATTGCAGCTCT-CCGGGACTACTTGAAAGTTGTAGATCTTTC
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGG-ACTACTTGAAGGTTGTAGATCTTTC
EST: gi|162179978|gb|FC356049.1|FC356049
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|162168515|gb|FC344452.1|FC344452
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|100431865|gb|BY978545.1|BY978545
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGNNTGTAGATCTT-CAGC
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGT-TGTAGATCTTTCAGC
EST: gi|67508394|gb|BJ941261.1|BJ941261
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|100379495|gb|BY949797.1|BY949797
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTTGA-GGTTGTAGATCTTTCAGC
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTT-GAAGGTTGTAGATCTTTCAGC
EST: gi|162234961|gb|FC411748.1|FC411748
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|100398471|gb|BY972624.1|BY972624
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACA-CTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGGAGGT
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGT
EST: gi|100445108|gb|BY964407.1|BY964407
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTT
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTT
EST: gi|100449342|gb|CJ973641.1|CJ973641
EST:     TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCANCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
EST: gi|100389059|gb|BY952263.1|BY952263
EST:     TCTCGCANGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAN                         GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG
genomic: TCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG

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: 21 (upstream exon), 33 (downstream exon)
Score: 14

GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtactt ... tatattgcagGAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAGgtgtgtacttgacagtgtatcttttgctaatcggtggagttctctcgttgttgtaggttgcgactgtatactgaggtgttcttttggtttctaccaggca

- - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA