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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaagaaaatttatcttaaaagtaatcagttagatttttttttctgtaacaatattgttaccatttttttttcttctcatttgtttaattgtgtttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAGCAGGGCCCGAGAAGCACCAAGCAGTGGCACTAAGATCAGACTCTGACCT

Basic information

species Glycine max
transcript GLYMA17G04940.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04940.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G33220.1 (Arabidopsis thaliana), 3'ss of exon 3
agaagaaaatttatcttaaaagtaatcagtta--gatttttttttctgtaacaatattgttaccatttttttttcttctcatttgtttaa----ttgtgt--------ttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAGCAGGGCCCGAGAAGCACCAAGCAGTGGCACTAAGATCAGACTCTGACCT
             |  ||| | |    ||||    |||  | |||   |||||||  ||||     |||| ||  |||| ||   ||| |    |||||         || |||| || || || ||||| ||| |||||||||| ||| | || ||||||||||||||||| |||||||| || || || ||||| |||||||||||||||||
------------gtaataagattttctagttgttaattcatgttttgataacaat--tgttttttcttttcttaattctaatggttttgaaacattgtgacacaaaaatttcagCGGTAAGCGGAAGAGGATTCTTAGCAAGAGATATAACGTTCCAGAACACAGCAGGGCCAGAGAAGCATCAGGCGGTAGCACTGAGATCAGACTCTGACCT
















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|19053310|gb|BM731977.1|BM731977
EST:     TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCG                         CTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
genomic: TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCGgtaagtatgc ... gtgtttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
EST: gi|6724360|gb|AW308759.1|AW308759
EST:     TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCG                         CTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
genomic: TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCGgtaagtatgc ... gtgtttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
EST: gi|15813955|gb|BI786230.1|BI786230
EST:     TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCG                         CTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
genomic: TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCGgtaagtatgc ... gtgtttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
EST: gi|7326760|gb|AW620558.1|AW620558
EST:     TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCG                         CTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
genomic: TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCGgtaagtatgc ... gtgtttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
EST: gi|14011926|gb|BG726848.1|BG726848
EST:     TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCG                         CTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG
genomic: TAACCGGAGTGTCGTCGACGGCTGGACCACCTTCCGCTCAGCTACATTCGgtaagtatgc ... gtgtttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacaatattgttaccatttttttttcttctcatttgtttaattgtgtttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAGCAGGGCCCGAGAAGCACCAAGCAGTGGCACTAAGATCAGACTCTGACCT
                 atttttttttcttctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaagaaaatttatcttaaaagtaatcagttagatttttttttctgtaacaatattgttaccatttttttttcttctcatttgtttaattgtgtttgcagCTGTGAGTGGCAGAGGGTTCATAGCAAGAGACATATCCTTTCAGAACACAGCAGGGCCCGAGAAGCACCAAGCAGTGGCACTAAGATCAGACTCTGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- aagaaaa
- - - - - - - - -aaaagtaa
- - - - - - - - - - - - - - - - - - - - -ttctgta