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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGTGTCGCTGGACATGCTTGGGCGTATCTTCAACGGATCTGGAAAACCTATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcag

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 6
CCAGTGTCGCTGGACATGCTTGGGCGTATCTTCAACGGATCTGGAAAACCTATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcag
 |||| ||  ||||||||||||| || || ||||| || ||||||||||| ||||| || ||||| ||||||||| | || || ||  | || || ||||||   |    ||   | || |   || |  ||   |   |  ||      ||||  ||||||||   || | | |                                       
-CAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATTTTACCTGAGGCTTACTTGGACATATCAGGtatataatttcttctggggaggtctgaatatgcatgtttttctttgccttttta-aatattttcc-ctgtaattcagg-----------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 6
CCAGTGTCGCTGGACATGCTTGGGCGTATCTTCAACGGATCTGGAAAACCTATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcag
||||| ||  ||||||||||||| || || ||||| || ||||||||||| ||||| || ||||| ||||| ||| | || || ||  | || || ||||||        ||   | || |    | |  ||   |   |  ||      ||||  ||||| |    | || | |                                       
CCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatttcttctggggaggtatgaatatgtatgtttatctttgcctttttt-aatatatccc-ccataattcag------------------------------------

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 5'ss of exon 6
CCAGTGTCGCTGGACATGCTTGGGCGTATCTTCAACGGATCTGGAAAACCTATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcag
|| || ||  |||||||||||||||| || || ||||| || ||||| || ||||| || || ||||| ||| |  ||||||| || ||||||||||||||||   |||        |  |    ||  | |  |      |  ||||  |||        ||||| ||   || ||  | |||| ||| |  |                    
CCTGTATCATTGGACATGCTTGGGCGCATATTTAACGGTTCAGGAAAGCCGATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAGgtga--gcaactaagaggacaattattccattgagatctctgaagcaatgtttca------tttgttcttaaaaatgtca-attccttatattgatag----------------

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|162269043|gb|FC445535.1|FC445535
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|18342277|gb|BJ174312.1|BJ174312
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|18368349|gb|BJ200434.1|BJ200434
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|162221566|gb|FC397583.1|FC397583
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|100425066|gb|BY976955.1|BY976955
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|100441292|gb|BY962581.1|BY962581
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|208357262|gb|DC910659.1|DC910659
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|100392297|gb|BY953293.1|BY953293
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|67574817|gb|BJ947641.1|BJ947641
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|162278567|gb|FC454029.1|FC454029
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|18357729|gb|BJ189788.1|BJ189788
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAN                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|100360601|gb|BY984200.1|BY984200
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|100432786|gb|BY978739.1|BY978739
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|100437022|gb|BY979644.1|BY979644
EST:     TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
EST: gi|100397347|gb|BY972453.1|BY972453
EST:     TACTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAG                         GTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA
genomic: TATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAA

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), 35 (downstream exon)
Score: 6

CCAGTGTCGCTGGACATGCTTGGGCGTATCTTCAACGGATCTGGAAAACCTATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcac ... gtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGTGTCGCTGGACATGCTTGGGCGTATCTTCAACGGATCTGGAAAACCTATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATCTTGATATTTCAGgtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC