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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCGGGGTGTCGAAAAGCGCATCGCAGGATGAGCTGAAGAGAGCATATAGGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccgagcattttggttgctgcaccttgaccgtgcgcttcctcgttttggctcgatttcgggcgtcgtctcattctcttgttcattttcattttt...

Basic information

species Physcomitrella patens
transcript PP1S342_16V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S342_16V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ24912 (Selaginella moellendorffii), 5'ss of exon 1
TCTCGGGGTGTCGAAAAGCGCATCGCAGGATGAGCTGAAGAGAGCATATAGGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccgagcattttggttgctgcaccttgaccgtgcgcttcctcgttttggct-cgatttcgggcgtcgtctcattctcttgttcattttcattttt
 || || || || ||    |  |||| ||| ||  ||||||  || ||  |||| || || ||||||||||||||||||||||| || ||||||||| ||||  ||         |||| |||| | |  |      |    | ||| |  ||| |   |||  |  |                                 
CCTTGGCGTCTCCAAGGATGTGTCGCCGGAGGATTTGAAGAAGGCGTACCGGAAGGCCGCCATCAAGAATCACCCGGACAAGGGAGGCGATCCCGAGCAGgtacgg------tgctttgtttgccggatttctcttttctcatgcctgggattgccggtgatccccag---------------------------------

upper sequence: PP1S342_16V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ30223 (Selaginella moellendorffii), 5'ss of exon 1
TCTCGGGGTGTCGAAAAGCGCATCGCAGGATGAGCTGAAGAGAGCATATAGGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccgagcattttggttgctgcaccttgaccgtgcgcttcctcgttttggct-cgatttcgggcgtcgtctcattctcttgttcattttcattttt
 || || || || ||    | ||||| ||| ||  ||||||  |||||  |||| || || |||||||||||||| |||||||| || ||||||||| ||||  ||         |||| |||| | |  |      |    | ||| |  ||| |   |||  |  |                                 
CCTTGGCGTCTCCAAGGATGTATCGCCGGAGGATTTGAAGAAGGCATACCGGAAGGCCGCCATCAAGAATCACCCCGACAAGGGAGGCGATCCCGAGCAGgtaagg------tgctttgtttgccggatttctcttttctcatgcctgggattgccggtgatccccag---------------------------------
















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|208359881|gb|DC939269.1|DC939269
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|100401219|gb|BY990892.1|BY990892
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|100414304|gb|BY992711.1|BY992711
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|162174909|gb|FC351701.1|FC351701
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|208380035|gb|DC914585.1|DC914585
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|162242594|gb|FC414985.1|FC414985
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|100359037|gb|BY946814.1|BY946814
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|162195909|gb|FC375642.1|FC375642
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|100357768|gb|BY946564.1|BY946564
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|208369628|gb|DC936362.1|DC936362
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|67507785|gb|BJ940663.1|BJ940663
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|100404490|gb|BY973604.1|BY973604
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGGCTTCCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCG
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAG-CTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCG
EST: gi|22492240|gb|BU052163.1|BU052163
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|100409753|gb|BY956088.1|BY956088
EST:     GGAAAGCGGCAACCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|100415464|gb|BY992856.1|BY992856
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|18329604|gb|BJ161610.1|BJ161610
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|162180208|gb|FC355525.1|FC355525
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|162185740|gb|FC362088.1|FC362088
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|208366024|gb|DC935841.1|DC935841
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|100448738|gb|CJ973037.1|CJ973037
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|67570938|gb|BJ943762.1|BJ943762
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
EST: gi|162162054|gb|FC338845.1|FC338845
EST:     GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAG                         TTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT
genomic: GGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGT

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: 105

TCTCGGGGTGTCGAAAAGCGCATCGCAGGATGAGCTGAAGAGAGCATATAGGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccg ... gctcttgcagTTCAAGGAGCTTTCCCAGGCATATGAGGTTTTGAGTGATCCCGAGAAGCGTGACTTGTATGATCAGTATGGGGAGGATGCCCTGAAGGAGGGGATGGGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCGGGGTGTCGAAAAGCGCATCGCAGGATGAGCTGAAGAGAGCATATAGGAAAGCGGCAATCAAGAATCACCCGGACAAGGGTGGAGATCCCGAGAAGgtgggggccgagcattttggttgctgcaccttgaccgtgcgcttcctcgttttggctcgatttcgggcgtcgtctcattctcttgttcattttcattttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC