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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcagactttttgggtactgattagtattactctcatttagttatgtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA

Basic information

species Glycine max
transcript GLYMA02G07830.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 14
--------------gtacgcagactttttgggtactgattagtattactctcattta-gtta----tgtaagcttacattcattat-tttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
               | | | |     |    || | ||     || | |   || | || |    | |   |||   |||  | | ||| || ||||| | ||||| || ||| | |||||||||||||| ||||| ||||| |||||||| ||| ||||||  ||||| ||||||||  | ||| |||||||||
gtaccaaaatctcaatgctctgttccatcttttatttatcttcttttccccggttcacgtcaaccttatcgactttttttccctgtgtttgtgtagAACTCATACCAGCAATATCTTGCTGCAAAAGAGCTGAAGAAACAGTCATGGAGATACCACAGGAAGTTCAACACTTGGTTTCAGAGACATAAAGAGCCAA

upper sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 14
gtac-gcagactttttg----ggtactgattagtatt-actctcatttagttat-------gtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
|||  |    |||| ||      | ||   |||| || ||  | || | |||||        ||  || |    ||||| |||||| |||| ||||| || || ||| ||||||||||||| ||||||||||| || |||||||| ||| |||| |||||||||||||||||  ||||||| |||||||
gtattgttagctttctgtaacaatccttcatagtgtttaccattatgtggttatcttgagcatattctcaagcgcattactttctgtagAATACTTATCAGCAATATTTGGCTGCAAAAGAACTAAAGAAGCAATCGTGGAGATACCACAGGAAATATAACACATGGTTTCAGAGGCATGAGGAGCCAA

upper sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S134_165V6.1 (Physcomitrella patens), 3'ss of exon 18
---------------gtacgcagactttttggg-------tactgatta-gtattactctcatttagttatgtaagcttacattcattatttt--ctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
               ||||  | ||| || | |       ||||| | |  || |||||  | || | | |      | |   ||     |||  || |||   || || || |||||  | || ||    ||| | || ||||| || ||| | ||||||   || || ||||||||||||||||| ||||||||||| |
tttgaggatgcatgagtacatacactattagtggcaatcctactgctaatatactactcaaactt-gctgttcgcattgattctctggggtttgactacagGGAACATATCAGCAGTACTTAGCAGCTCGGGAGTTGAAAAAGCAATCATGGCGGTATCACAAAAAATACAACACATGGTTTCAACGTCATGAAGAGCCCA

upper sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ20408 (Selaginella moellendorffii), 3'ss of exon 12
gtacgcagactttttgggtactgattagtattactctcatttagttatgtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
                 ||  || |   | ||||  ||  ||   ||   |     ||     || | |  | |||   || ||||| |||||| | || ||||  ||||||||||| || || ||||||||||||  |||||| ||||||||||| || || || || ||||| |
-----------------gtg-tgctctcttttacattctgttctgtacaaattaccacgggttttgtgtctttcagGGAACGTACCAGCAGTATCTAGCCGCAAGGGAGCTAAAGAAACATTCGTGGAGATATCACAAGAAGTACAACACATGGTTCCAGCGCCACGAGGAGCCGA

upper sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ28394 (Selaginella moellendorffii), 3'ss of exon 2
gtacgcagactttttgggtactgattagtattactctcatttagttatgta-agcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
                      |  |  | |   |  ||||  ||| |||| |  ||||        |||| | |||   || ||||| |||||| | || ||||  ||||||||||| || || ||||||||||||  |||||| ||||||||||| || || || || ||||| |
----------------------gtgtgctctcttttacattctgttctgtacaaattaccacgg--gttttgttcagGGAACGTACCAGCAGTATCTAGCCGCAAGGGAGCTAAAGAAACATTCGTGGAGATATCACAAGAAGTACAACACATGGTTCCAGCGCCACGAGGAGCCGA

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|7590888|gb|AW706631.1|AW706631
EST:     TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtacgcagac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|208230983|gb|GE033102.1|GE033102
EST:     TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAA
genomic: TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtacgcagac ... ttttctgcagAACACTTACCAA
EST: gi|193602394|gb|FK556291.1|FK556291
EST:     TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGG
genomic: TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtacgcagac ... ttttctgcagAACACTTACCAACAGTATATGG
EST: gi|254336764|gb|GR842943.1|GR842943
EST:     TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtacgcagac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|13481733|gb|BG511076.1|BG511076
EST:     TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtacgcagac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattagtattactctcatttagttatgtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
                                          ttattttct  CT-rich tract
                                 ttacattcattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcagactttttgggtactgattagtattactctcatttagttatgtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA