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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatagcttctcctccatgtgctccttcatgaacctattgttttggtatttgtttgtggatgtgtgtctttggtttgattgtttagGAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCATGTGGACATGATGCTCACACCACCATGCTACTTGGGGCTGCAAAGTTGC

Basic information

species Glycine max
transcript GLYMA04G40440.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40440.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G54140.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgatagcttctcctccatgtgctccttcatgaacctattgttttggtatttgtttgtggatgtgtgtctttggtttgattgtttagGAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCATGTGGACATGATGCTCACACCACCATGCTACTTGGGGCTGCAAAGTTGC
    ||   ||  || |     |||  || |  |    |||||      ||  | ||| |||       |||| || |||| || |||| |||||||||||||| || ||||||||||| || || | ||||||||| ||||| |||||| |||| ||||| ||||| ||||| ||||| || ||||
---gtaaactcgacttctctctctctctctttgattgtttgtt---aatttcttctgtagattga----tttgcttcgatttttcagGAACTTGTTGAGTGGGATCATAAGAGCAAAATCGATGGAAAAATGCATGCTTGTGGTCATGATTCTCATACCACTATGCTCCTTGGTGCTGCTAAATTGC

upper sequence: GLYMA04G40440.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0098g00770.t01 (Vitis vinifera), 3'ss of exon 1
gtgatagcttctcct-ccatgtgctccttcatgaacctattgttttggtatttgtttgtggatgtgtgtctttggtttgattgtttagGAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCATGTGGACATGATGCTCACACCACCATGCTACTTGGGGCTGCAAAGTTGC
     | || |  |     || | |   |   |||  |  |    |||  |||||||   ||| ||  | | |||||||      |||||||||||||||||||| || |||||||| ||||| || | ||||||||  || ||||| ||||| |||||||| ||||| || |||||||| |||||||
---gcacctacaacagttttgagttagattgagaatttggttggatgggttttgtttt--gatttgcttttatggtttg------tagGAGCTTGTTGAGTGGGAGCATAAGAGCAAGATTGATGGGAAAATGCATGGGTGCGGACACGATGCCCACACCACTATGCTGCTGGGGGCTGCCAAGTTGC

upper sequence: GLYMA04G40440.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0098g00780.t01 (Vitis vinifera), 3'ss of exon 2
gtgatagcttctcctccatgtgctccttcatgaacctattgttttggtatttgtttgtggatgtgtgtctttggtttgattgtttagGAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCATGTGGACATGATGCTCACACCACCATGCTACTTGGGGCTGCAAAGTTGC
||     |  |   |   || | |   |   |||    ||| || | |  || | | | ||| ||  | | ||||||      ||||||||||||||||||||| || |||||||| ||||| || | ||||||||  || || || ||||| |||||||| ||||| || || ||||| |||||||
gtacccacagcagttt--tgagttagattgagaat---ttggttggatggttttgttttgatttgcttttatggttt------ttagGAGCTTGTTGAGTGGGAGCATAAGAGCAAGATTGATGGGAAAATGCATGGGTGCGGCCACGATGCCCACACCACTATGCTGCTCGGTGCTGCCAAGTTGC

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|14999998|gb|BI320812.1|BI320812
EST:     CTCGCCCCATCATTGCTATTCGTGCTGACATTGATGCACTCCCCATGCAG                         GAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCA
genomic: CTCGCCCCATCATTGCTATTCGTGCTGACATTGATGCACTCCCCATGCAGgtgatagctt ... gattgtttagGAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCA
EST: gi|209708930|gb|BW673912.1|BW673912
EST:     CTCGCCCCATCATTGCTATTCGTGCTGACATTGATGCACTCCCCATGCAG                         GAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCA
genomic: CTCGCCCCATCATTGCTATTCGTGCTGACATTGATGCACTCCCCATGCAGgtgatagctt ... gattgtttagGAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctattgttttggtatttgtttgtggatgtgtgtctttggtttgattgtttagGAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCATGTGGACATGATGCTCACACCACCATGCTACTTGGGGCTGCAAAGTTGC
                                         gtttgat  putative branch site (score: 5)
               tatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatagcttctcctccatgtgctccttcatgaacctattgttttggtatttgtttgtggatgtgtgtctttggtttgattgtttagGAGCTTGTTGAGTGGGAACACAAGAGCAAAATTGAGGGCAGAATGCATGCATGTGGACATGATGCTCACACCACCATGCTACTTGGGGCTGCAAAGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG