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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCAGAGGCTGCAAGAATTCGTGACAAGTATCCCGACAGAATCCCAGTGATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggtttttaccactcttttttgtgtgtgtgtgcgtgtgtgtgttttttcatagttggagggcacttggtcaccttcgggtattagttttggtatggttatttatcattctgacggtacatttttgtcatgtgatctgaagttgggcacatgtagcatagatattgaaagtgatgaatgaatgtgtttgcag

Basic information

species Physcomitrella patens
transcript PP1S26_103V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S26_103V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA15G11510.1 (Glycine max), 5'ss of exon 3
AGGCAGAGGCTGCAAGAATTCGTGACAAGTATCCCGACAGAATCCCAGTGATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggtttttaccactcttttttgtgtgtgtgtgcgtgtgtgtgttttttcatagttg--gagggcacttggtcaccttcgggtattagttttggtatggttatttatcattctgacggtacatttttgtcatgtgatctgaagttgggcacatgtagcatagatattgaaagtgatgaatgaatgtgtttgcag
                                               |||||||||||||| || || | ||| ||||| |||||||||||||||||||||||       |    | || ||  |   | ||| | | |   |   ||| ||    ||   | |    || |   |||    || ||| |  |  | ||| |                                                                                             
-----------------------------------------------GTGATTGTGGAGAAAGCTGAAAGAAGTGACATTCCAGACATTGATAAGAAAAAgta-------attgattttcttactacttctgtcccttttgattagtttccaggcctgataatgttgttttgctgcctg-aagttttaatgattttgtgggtgggggg---------------------------------------------------------------------------------------

upper sequence: PP1S26_103V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA09G00630.2 (Glycine max), 5'ss of exon 4
AGGCAGAGGCTGCAAGAATTCGTGACAAGTATCCCGACAGAATCCCAGTGATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggt--ttttaccactcttttttgtgtgtgtgtgcgtgtgtgtgttttttcatagttggagggcacttggtcaccttcgggtattagttttggtatggttatttatcattctgacggtacatttttgtcatgtgatctgaagttgggcacatgtagcatagatattgaaagtgatgaatgaatgtgtttgcag
                                               |||||||||||||| || || | ||| ||||| || |||||||||||||||||||  |   ||||   |  || ||| ||   | | ||  |   |   |  | |  |  ||         || |   |||   ||  ||  ||| ||  ||| |                                                                                             
-----------------------------------------------GTGATTGTGGAGAAAGCTGAAAGAAGTGACATTCCTGACATTGATAAGAAAAAgtgagcgattttcttatgctatttcgtcccttt-tgattagtttcctggtctggtgattt-----tgttttgctgcctgaagggttttatttgggggtgggtgggg-----------------------------------------------------------------------------------------
















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|18344066|gb|BJ176105.1|BJ176105
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|162186577|gb|FC363341.1|FC363341
EST:     GTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: GTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|37821375|gb|BJ579441.1|BJ579441
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|67571088|gb|BJ943912.1|BJ943912
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|67571800|gb|BJ944624.1|BJ944624
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|162232018|gb|FC409092.1|FC409092
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|162232017|gb|FC409091.1|FC409091
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|18352101|gb|BJ184155.1|BJ184155
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|208374917|gb|DC956190.1|DC956190
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|162262025|gb|FC437872.1|FC437872
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|37823258|gb|BJ581324.1|BJ581324
EST:     ACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|18327459|gb|BJ159462.1|BJ159462
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|67694401|gb|BJ954634.1|BJ954634
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|37831787|gb|BJ589799.1|BJ589799
EST:     ATTGT-GAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|18331908|gb|BJ163920.1|BJ163920
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|100376476|gb|BY986185.1|BY986185
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|162254652|gb|FC429502.1|FC429502
EST:     GAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: GAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|67695168|gb|BJ955401.1|BJ955401
EST:     GAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: GAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|18342266|gb|BJ174301.1|BJ174301
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|37821564|gb|BJ579630.1|BJ579630
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|162276592|gb|FC451975.1|FC451975
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
EST: gi|162202124|gb|FC377525.1|FC377525
EST:     ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAA                         GTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG
genomic: ATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAG

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: 34 (upstream exon), 33 (downstream exon)
Score: 46

AGGCAGAGGCTGCAAGAATTCGTGACAAGTATCCCGACAGAATCCCAGTGATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggttttt ... gtgtttgcagGTACCTGGTACCAGCGGACTTGACGGTTGGACAGTTCGTATATGTGATAAGGAAGCGCATCAAATTGAGTTCCGAAAAGGCCATTTTCATCTTCGTGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCAGAGGCTGCAAGAATTCGTGACAAGTATCCCGACAGAATCCCAGTGATTGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATTGATAAGAAAAAgtaggtttttaccactcttttttgtgtgtgtgtgcgtgtgtgtgttttttcatagttggagggcacttggtcaccttcgggtattagttttggtatggttatttatcattctgacggtacatttttgtcatgtgatctgaagttgggcacatgtagcatagatattgaaagtgatgaatgaatgtgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA