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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagagagagagagagagagagaggctctttaccttctcgtgtttcaatttgaatttctgttaaatattattttgttagggttggaaacttgaaatgaacgtgtggtgtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTT

Basic information

species Glycine max
transcript GLYMA04G36420.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36420.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagagagagagagagagagagaggctctttaccttctcgtgtttcaatttgaatttctgttaaatattattttgttagggttggaaacttgaaatgaacgtgtggtgtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTT
            | |    |  |     ||||    ||| || ||  | |||   |  ||   |   || ||| ||||    |        ||   ||||  | |||| |  ||  ||||||| || |||||||| ||||| || ||||| || ||||||||||| || |||||||| ||||||||||| ||||| || || ||||| |||| | |||
-----------tgtgtttcatgggtctgctttgaaatctggttttatagtttatttggcttaaaggaatgattatgtt----tcatgggtctgctttgaa-atctggttt--ttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTT

upper sequence: GLYMA04G36420.2 (Glycine max), 3'ss of exon 1
lower sequence: AT4G24770.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagagagagagagagagagagaggctctttaccttctcgtgtttcaatttgaatttctgttaaatattattttgttagggttggaaacttgaaatgaacgtgtggtgtggtttta-gGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTT
               | |      | |  | ||| ||    | | ||  ||| | ||  |   | | || || |||||||   ||   |||||   |     | |  ||||||| || |||||| || ||||||||||||||||||||||| || ||||| |||||||| |||||| | || || ||||||||||  || |||||||| ||||  ||||
---------------atatctgttgacattatacttttggttctctcttttttatttagttcaagagataatgttgttagtcctg---acttgttctttgaat-tcttgtggttgtaagGTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTT

upper sequence: GLYMA04G36420.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g09680.t01 (Vitis vinifera), 3'ss of exon 1
gtcagagagagagagagagagagaggctctttaccttctcgtgtttcaatttgaatttctgttaaatattattttgttagggttggaaacttgaaatgaacgtgtggtgtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTT
                                    |   |   |||  |||| | || |||| | | |     | |  ||||   | |    |  ||   || || |    ||  |||||||||| |||||||| |||||    ||||| || || ||||||||| | |||||||| ||||||||||| || || || ||||| |  ||   |||||
---------------------------------gtatggagctgttcggtttggaatt-tgttgattttggggatttgggggt---atatcatatctgggtgtttgcttgttttgcagGTTATTTACAATAGGGAGACTGATAGAAGTCGTGGGTTCGGGTTTGTGTCAATGAGTACTGTTGAAGAAGCCGAAAAGGCTGTGGATATGTTTCATCGTT

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|8403170|gb|BE058804.1|BE058804
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
EST: gi|23058133|gb|BU578293.1|BU578293
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
EST: gi|17023176|gb|BM094210.1|BM094210
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
EST: gi|15204745|gb|BI427513.1|BI427513
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
EST: gi|18848478|gb|BM567697.1|BM567697
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
EST: gi|15286229|gb|BI470120.1|BI470120
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
EST: gi|7590995|gb|AW706737.1|AW706737
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
EST: gi|23728471|gb|BU762290.1|BU762290
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
EST: gi|298191349|gb|HO038828.1|HO038828
EST:     AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAG                         GTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG
genomic: AGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagaga ... gtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatattattttgttagggttggaaacttgaaatgaacgtgtggtgtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTT
     ttattttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagagagagagagagagagagaggctctttaccttctcgtgtttcaatttgaatttctgttaaatattattttgttagggttggaaacttgaaatgaacgtgtggtgtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA