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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcctagagaatttagcaagagtcacacaactcaatctcttttgtgaagtttttggtttggtccattttgcatgatatggttatgctatttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG

Basic information

species Glycine max
transcript GLYMA13G01360.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 9
lower sequence: AT4G30340.1 (Arabidopsis thaliana), 3'ss of exon 6
ctgcctagagaatttagcaagagtcacacaactcaatctcttttgtgaagtttttggtttggtccattttgcatgatatggtta-tgctatttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG
            || |   | |       ||    |||| |  |   || |       | | | || ||   || || |   |  |  | |||   |  || |||||  | || || |  ||||||||| ||| |||||||||||||||| ||||||||||||| |  | |||| ||||||| || |||
-----------gttcatataaaact----aatcttatctttgattaaaactaaaaaaatggcttcactt---ataatctctctggttttgttttggtgtagCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG

upper sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 7
ctgcctagagaatttagcaagagtcacacaactcaatct---cttttgtgaagtttttggtttggtccattttgcatgatatggttatgctatttccttt--cagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG
 |  ||| ||||  ||| || |   |||||| | |  |    |  || | ||  |  |  || |||   |  || | ||| ||  | ||||  ||  |    ||||||||| ||| | ||||| |||||||| ||||||||||||||||||||||| || ||||| || |  |||| ||| ||| | ||||| 
gtatctacagaa--tagaaacaagaacacaaatgagacagaacacttttaaatctcataattgggtttctaatgaaagatgtgtgtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA

upper sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 9
lower sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 9
ctgcctagagaatttagcaagagtcacacaactcaatctcttttgtgaagtttttggt-ttggtccattttgcatgatatggttatgctatttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG
            |  |  |    |  |   |    || | | |  |  | | |||| | |   | | |    | ||||   | ||||   ||  |||  ||||| ||  |||| || || ||||||||||| |||||||||||||||||  |||| ||||| || | |||||| || ||| | || |||
-----------gtaaaaaacagttttcgatatatgatttatgtattacaatctttgatatcaatgcttaaaacctgat---gctatggatttctcttgtagTGTGAGATCAATTGTCGCATTGAATCTTCACAGCTATGGAAGTGGAAGCCATCCTTGGGGCAATCTAAAACCGGACTATCTAGAGAAG

upper sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
ctgcctagagaatttagcaagagtcacacaactcaatctct-tttgtgaagtttttggtttggtccattttgcatgatatggttatgctatttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG
|    |||  |  ||        |   |   ||   |||   ||| | |    | |  |||  | |||||    | |  |  |  | || |   |||  ||||| ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| |  || ||||| ||||||||||||
caaaatagcaacctttttttattttttatttctttttcttgatttattattagtatcattta-ttcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG

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|208159309|gb|GD954260.1|GD954260
EST:     ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAG                         TGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
genomic: ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAGgtacttttct ... ttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
EST: gi|192332064|gb|FK026344.1|FK026344
EST:     ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAG                         TGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
genomic: ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAGgtacttttct ... ttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
EST: gi|51337091|gb|CO980957.1|CO980957
EST:     ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAG                         TGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
genomic: ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAGgtacttttct ... ttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
EST: gi|302141303|gb|HO212179.1|HO212179
EST:     ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAG                         TGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAGGAAA
genomic: ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAGgtacttttct ... ttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
EST: gi|15203215|gb|BI425983.1|BI425983
EST:     ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAG                         TGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGTAAGAAA
genomic: ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAGgtacttttct ... ttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
EST: gi|192332065|gb|FK026345.1|FK026345
EST:     ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAG                         TGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA
genomic: ATCAAAAGGGCCAATAGCTCAGAGTGGGAGCAGATTGCAATTCCTACAAGgtacttttct ... ttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagtttttggtttggtccattttgcatgatatggttatgctatttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG
                                       tgctatttcctttc  CT-rich tract
                           atgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcctagagaatttagcaagagtcacacaactcaatctcttttgtgaagtttttggtttggtccattttgcatgatatggttatgctatttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA