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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC

Basic information

species Glycine max
transcript GLYMA08G24120.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 12
gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttg-acagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
        ||||||    |  | |||  |||  || |  ||     ||  |  | | |       |  |         |||| | ||   ||||| ||||| ||||| || ||||| ||||| |||||||| ||||| ||||||||||| || || || |||||||  || || ||||| || || || ||||
--------gtgagtacatgcatataat-taagtttgt-catttttcttatgcctataaaagttaatgctaacttctaatataatgttatgcagGACTACAACGAGAAGCCTGATTACGGTCGTTGTGTTGCAATTGTGGCATCTGCTTCCTTGAGGGAAATGATAAGGCCGGGGGCTTTAGCCATTATATCAC

upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 12
gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcg-attttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
               || ||   | |  ||  || | ||    ||||||     || ||  | |   |  |  | |||    |  |    ||||| ||||| ||||| || |||||||| |||||||| || ||||| || ||||| || |||||||| |||||||||||||| ||| | ||||| || ||||
--------------gtgagtgcatgat-taccatgaagttcttcagttttatgcttggaaaagctgatgctaacttgtaacaatatcatccagGACTACAAAGAGAAGCCCGATTATGGACGCTGTGTCGCAATTGTGGCCTCTGCATCCTTAAGAGAAATGATAAAACCTGGGGCTCTAGCAATTATATCAC

upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G069410_T01 (Zea mays), 3'ss of exon 4
gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
        ||||||    | ||   | | | |  |      | |  |||    || ||  | |   |  |  | |||    |  |    ||||| ||||| ||||| || |||||||| ||||||||||| ||||| |||||||| || || ||||| |||||||| ||||| ||| | ||||| || ||||
--------gtgagtacatgattaccatgaagttcttca---gtccttttatgcttggaaaagcagatgctaacatgtaacaatatcatccagGACTACAAAGAGAAGCCGGATTATGGACGCTGTGTTGCAATTGTGGCATCTGCATCCTTGAGAGAAATGATAAAGCCTGGAGCTCTAGCAATTATATCAC

upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 12
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 13
gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
        || | | |   |  |          ||   | | |   |||  |||||  | | ||  | | ||  ||    |   | | |||||| ||||||||||| |||||||||||||| ||||| || ||||| |||||| |  | || || || ||||||||||| || |||||||| || || ||||
--------gtaaatgtaattccgctggagtccgttccctttta---tttttatttttttcatcgggtgtctttttgaactt-tatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC

upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 12
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 12
----gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
    | ||| |  |   |||| ||   | |  |  | || |||||     ||      ||| ||||       | || ||||           ||||| ||||||||||| ||||||||| |||||||||| || || || ||||||||  | |||||||| |||||||| || || ||||| || ||    ||||
gtgagcatatttttccttttgagtgcttcaccttttcttgtgtattg-gcttgtaccgttgttgactagcaaatatcttgtt----------gcagGAGTACAAGGAGAAGCCAGATTATAGTCGCTGTGTCGCCATAGTCGCATCTGCAGCTTTAAGAGAAATGATAAAGCCAGGAGCTTTAGCTATTGCATCAC

upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 12
----gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgatttt-gatgaccgctttttttcctgtttatacttttg--acagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
    |||| ||  |   |  |  ||| ||  ||  ||| ||| |||   ||||  |||||  ||    || |    |  | || | |  ||||  |||||| || || ||||||||||| |||||||| |||||||| |||||||||||||| ||  | || |||||||||||||| ||||||||||| ||  | ||||
gtgagtatgattctctata-gcatttttatggtt-tatcatgaatgtaggttttaatttttaattgatgcatgaaattgttttaacatgtttgctacagGACTATAAAGAGAAACCAGACTATGGTCGTTGTGTTGCCATTGTAGCATCTGCATCTCTGAGGGAGATGATAAAACCCGGTGCTTTGGCTATTGTATCAC

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|58022340|gb|CX709081.1|CX709081
EST:     TGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTG                         GATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCT
genomic: TGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGgtataatggt ... cttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCT
EST: gi|120529405|gb|EH257539.1|EH257539
EST:     TGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGGTATAATG                  
genomic: TGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCC--------TGgtataatggt ... ctt
EST: gi|58022630|gb|CX709371.1|CX709371
EST:     TGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTG                         GATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCT
genomic: TGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGgtataatggt ... cttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
               ttttgat  putative branch site (score: 4)
                           ctttttttcctgttta  putative PPT
                                       tttatactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG