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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgcacgcgttgtgcgcaaatagtgaaacttatatgccagagtcttagacatgttctttttttggagatgattttaatattgggattatgtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTAGATGAGATGATCCGCGAGGCCGATGTGGATGGTGACGGCCAGGTCGACT

Basic information

species Physcomitrella patens
transcript PP1S58_258V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_258V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ32870 (Selaginella moellendorffii), 3'ss of exon 3
gttgcacgcgttgtgcgcaaatagtgaaacttatatgccagagtcttagacatgttctttttttggagatgattttaat--attgggattatgtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTAGATGAGATGATCCGCGAGGCCGATGTGGATGGTGACGGCCAGGTCGACT
                       |||| |   ||      || |||| | | ||||  |  |||        |||| |   | ||| |||   |      || |  || ||||||||| ||| ||||| || |||||||| ||||| || ||||| ||||||||||||||||| ||  |||| || ||||| || ||  |||
-------------------gtctgtgagagacatg-----gattcttggtcttgtttctcgttt-----cctttttgactgactggaatttctt---cccagTTGAGGGACGTGATGATCAATCTGGGCGAGAAGCTGACCGACGAGGAGGTAGAAGAGATGATCCGCGAGGCTGACATGGACGGCGACGGTCACGTTAACT

upper sequence: PP1S58_258V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ14591 (Selaginella moellendorffii), 3'ss of exon 3
gttgcacgcgttgtgcgcaaatagtgaaacttatatgccagagtcttagacatgttctttttttggagatgattttaat--attgggattatgtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTAGATGAGATGATCCGCGAGGCCGATGTGGATGGTGACGGCCAGGTCGACT
                       |||| |   ||      || |||| | | |||| ||  |||        |||| |   | ||| |||   |      || |  || ||||||||| ||| ||||| || |||||||| ||||| || ||||| ||||||||||||||||| ||  |||| || ||||| || ||  |||
-------------------gtctgtgagagacatg-----gattcttggtcttgtttttcgttt-----cctttttgactgactggaatttctt---cccagTTGAGGGACGTGATGATCAATCTGGGCGAGAAGCTGACCGACGAGGAGGTAGAGGAGATGATCCGCGAGGCTGACATGGACGGCGACGGTCACGTTAACT
















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|162270598|gb|FC446523.1|FC446523
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|6166882|gb|AW145146.1|AW145146
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|162207454|gb|FC383699.1|FC383699
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|18329931|gb|BJ161937.1|BJ161937
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACTTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|208373251|gb|DC948553.1|DC948553
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|67570099|gb|BJ942923.1|BJ942923
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|162231888|gb|FC408754.1|FC408754
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|162278520|gb|FC453982.1|FC453982
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|18343994|gb|BJ176033.1|BJ176033
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|162244646|gb|FC424613.1|FC424613
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|162207453|gb|FC383698.1|FC383698
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|37823186|gb|BJ581252.1|BJ581252
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|67698429|gb|BJ958662.1|BJ958662
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|37847801|gb|BJ605809.1|BJ605809
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|208362046|gb|DC943487.1|DC943487
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|19790467|gb|BQ041885.1|BQ041885
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|67574994|gb|BJ947818.1|BJ947818
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
EST: gi|162244647|gb|FC424614.1|FC424614
EST:     CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAG                         CTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA
genomic: CGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTA

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: 32 (upstream exon), 33 (downstream exon)
Score: 8

GATACCGACTCTGAGGAGGAGTTGAAGGAAGCGTTTAAAGTATTCGATAAGGATCAGAATGGCTTCATCTCTGCTGCGGAGgtcagtctcg ... gtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTAGATGAGATGATCCGCGAGGCCGATGTGGATGGTGACGGCCAGGTCGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagacatgttctttttttggagatgattttaatattgggattatgtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTAGATGAGATGATCCGCGAGGCCGATGTGGATGGTGACGGCCAGGTCGACT
                           ttttaat  putative branch site (score: 8)
                     agatgattttaatatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcacgcgttgtgcgcaaatagtgaaacttatatgccagagtcttagacatgttctttttttggagatgattttaatattgggattatgtgaatgaagCTCCGGCACGTGATGACCAACCTGGGGGAAAAGCTGACAGACGAAGAAGTAGATGAGATGATCCGCGAGGCCGATGTGGATGGTGACGGCCAGGTCGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG