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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catccatttgaaagaactataatgaagcttaatcttgcaaccactttttttgtcttaatttttttgggtataaaagtagtgcaatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC

Basic information

species Glycine max
transcript GLYMA02G01060.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 8
--catccatttgaaagaactataatgaagcttaatcttgcaaccactttttttgtcttaatttttttgggtataaaagtagtgcaatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
       || ||    ||   |    |  |  || ||    |   | |||  |  |  |       | |    ||  ||  | |  |   | |    | ||||| || ||||| |||||||| ||||| |||||||| |||||||||||||| |||||||| || ||||| |||||||||||||| ||||||||||| || |
tctgattatgtgcttcaaactttggaagccacaagctcatgatttcatttcctaacacatcgaaaatcgtctcaa--gttttactttgaatttgtactgtagGTCCTCAATGCTAAACCAGAGAATGTAGAGAGGGAGGCAGAAATTGTAGCTCAGAGTGGACGCCTTGGTGCAGTGACAATTGCCACCAATATGGCGGGAC

upper sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 10
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 9
---catccatttgaa---agaactataatgaagcttaatcttgcaaccactttttttgtcttaatttttttgggtataaaagtagtgcaatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
     |  || | ||   | | | ||||  ||    |||    |||  |  ||  ||||   |   |  |     || |  ||  |  | |||||  |      |||| || ||||| || ||||||||||| ||||||||||| |||||||||||||| ||||| ||| | |||||||| |||||||| || |||||||| || |
aatggtgtatgtaaagacaaaccaataaaaaaatcaaat----caattatattccttgtacaagaatactgacagatgat-gttatata-tatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC

upper sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 10
-catccatttgaaagaactataatgaagcttaatcttgcaaccactttttttgtcttaatttttttgggtataaaagtagtg--caatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
        || |     || |  ||  ||  ||  | || |  |  |  | | ||| ||| ||  | |    | |  || |    |||||   ||  ||  |||| || ||||| |||||||| ||||| ||||| |||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||
atgctatatttatgtttctcttttgctgcc-aacatagcca--aactactatatctaaatattcgttgtatgagatatattaactaatatcatttaattaaagGTTCTCAATGCGAAACCAGAGAATGTAGAGAGAGAAGCAGAAATTGTTGCACAGAGTGGTCGTCTTGGGGCAGTTACAATTGCTACCAATATGGCAGGTC

upper sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 10
lower sequence: PP1S9_141V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------------------------------catccatttgaaagaactataatgaagcttaatcttgcaaccactttttttgtcttaatttttttgggtat----aaaagtagtgcaatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
                                                                                             | | |     |  ||||    | |  |   |  ||   |  ||        |    | |||||||     |    |      ||   | ||| |||  ||  ||||||| ||||| ||||||||||| || || || ||||| |||||||| |||||||| || ||  | || || |||||||| ||||| || ||||||||||
gtgacattcgtgttcttttaagtaggcgcgaatcacctaaaaattttagaattaggattaggttaattttctagctaatcatcataataatttcgtgcgcagaagggaacctggaggctggccagactctaattcagaagagacggtgcattttttttaaagcttcccactgaatgtttgagatg-attccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCACAGAGCGGGCGCTTAGGAGCCGTGACAATAGCTACGAACATGGCTGGTC

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|7692056|gb|AW760172.1|AW760172
EST:     AGAGTGATTCTTTGTCAGAGCAATTGAAAGAAGCTGGAATTCCGCACGAG                         GTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCA
genomic: AGAGTGATTCTTTGTCAGAGCAATTGAAAGAAGCTGGAATTCCGCACGAGgtaaggtccc ... ttgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCA
EST: gi|23731376|gb|BU763804.1|BU763804
EST:     AGAGTGATTCTTTGTCAGAGCAATTGAAAGAAGCTGGAATTCCGCACGAG                         GTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCA
genomic: AGAGTGATTCTTTGTCAGAGCAATTGAAAGAAGCTGGAATTCCGCACGAGgtaaggtccc ... ttgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCA
EST: gi|16278936|gb|BI943171.1|BI943171
EST:     AGAGTGATTCTTTGTCAGAGCAATTGAAAGAAGCTGGAATTCCGCACGAG                         GTACTTAATGCACAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCA
genomic: AGAGTGATTCTTTGTCAGAGCAATTGAAAGAAGCTGGAATTCCGCACGAGgtaaggtccc ... ttgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgtcttaatttttttgggtataaaagtagtgcaatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
       tcttaat  putative branch site (score: 3)
                                             ttgtttct  putative PPT
         ttaatttttttgggta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catccatttgaaagaactataatgaagcttaatcttgcaaccactttttttgtcttaatttttttgggtataaaagtagtgcaatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC

catccat
- - - - -gaaagaac
- - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - -tgcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtgcaa