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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTATCTCGGCCATTGAGTTCGATAAAACTGGAGAGCATTTGGCAACTGGAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctgtttcatgtcgttgttcttaatccatgctggtacctgttcttagtgtccagtgatatgtttatctagtgcatactatctgtgctggcgtca...

Basic information

species Physcomitrella patens
transcript PP1S301_53V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 2
CATTATCTCGGCCATTGAGTTCGATAAAACTGGAGAGCATTTGGCAACTGGAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctgtttcatgtcgttgttcttaatccatgctggtacctgttcttagtgtccagt--gatatgtttatctagtgcatactatctgtgctggcgtca
||| ||||| || || |||||| ||||| | ||| | ||| | || ||||||||| ||||||||||||||||| | ||||| || || |||| || ||||||| |     | |      ||    |  | ||  ||| |     |   ||  || | |||   | ||    ||| | ||   |  | |||    |       
CATCATCTCAGCAATAGAGTTCAATAAATCAGGACATCATCTTGCCACTGGAGACAGAGGTGGACGAGTTGTTTTATTTGAAAGGACCGATGTCAAAGATgtatgc---atattgaactgtacaccaaagtc--tgcagactttttccctctgtattcagatggctaaacatattttgtttgttttttcttcctttag----

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 2
CATTATCTCGGCCATTGAGTTCGATAAAACTGGAGAGCATTTGGCAACTGGAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacg-----ttctgtttcatgtcgttgttcttaatccatgctggtacctgttcttagtgtccagtgatatgtttatctagtgcatactatctgtgctg-gcgtca-----
||| || || || ||||| || || ||  |||| || ||| | || ||||| || |||||||| ||||| ||||||||||||||||| |||   | ||||||| |     || |   | |||    |||| ||     |       |       |  ||  |  || ||    |||  || || |   | | |||  |  |   ||     
CATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGAGGTGGTCGAGTGGTTCTCTTTGAGAGAACAGATACAAAAGATgtaagactattttttgcttatgcaagtgtttttgtgtaaaaaaaaaaaaccaaataggttccttgttatgcacttaa-tattgtaacatgtatgttttctgaaacatgcag
















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|100404937|gb|BY991356.1|BY991356
EST:     GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGAT                         CAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
genomic: GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctg ... gtctttgcagCAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
EST: gi|100446612|gb|CJ970911.1|CJ970911
EST:     GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGAT                         CAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
genomic: GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctg ... gtctttgcagCAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
EST: gi|162155365|gb|FC331979.1|FC331979
EST:     GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGAT                         CAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
genomic: GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctg ... gtctttgcagCAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
EST: gi|18347719|gb|BJ179766.1|BJ179766
EST:     GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGAT                         CAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
genomic: GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctg ... gtctttgcagCAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
EST: gi|162152096|gb|FC328686.1|FC328686
EST:     GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGAT                         CAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT
genomic: GAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctg ... gtctttgcagCAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACAT

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), 29 (downstream exon)
Score: 16

CATTATCTCGGCCATTGAGTTCGATAAAACTGGAGAGCATTTGGCAACTGGAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctg ... gtctttgcagCAAAGGACACGAAGAGAGTTAGAAAGGGCTGATTTTGTGGGTCCAAGACATCCAGAATATCGATACTCAACTGAGTTTCAAAGTCACGAGCCAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTATCTCGGCCATTGAGTTCGATAAAACTGGAGAGCATTTGGCAACTGGAGACCGAGGTGGACGAGTTGTTCTCTTTGAGAGAACGGATGGCAGAGATgtacgttctgtttcatgtcgttgttcttaatccatgctggtacctgttcttagtgtccagtgatatgtttatctagtgcatactatctgtgctggcgtca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA