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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaaacctttgttgtttgttggtaatgatggtaatcttttctattttttctgtttccttttctcgaccccctgggctttgattgagtcactaaatgcagGTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAAGAGCTTCAG

Basic information

species Glycine max
transcript GLYMA10G37690.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G37690.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00800.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------caaaaacctttgttgtt----tgttggtaatgatggtaatctt--ttctattttttctgtttccttttctcgaccccctggg-ctttgattgagtca-ctaaatgcagGTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAAGAGCTTCAG
                                                                      | |||  || ||      ||     |||  |||||  |  ||  |     |  | |||  | | | | |     |   ||||| ||   | | || ||||||||||||| | ||| ||||||| || ||||||  |||||| ||||| |||||||||||||| 
gtaatctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaattattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAAGAGCTTCAA
















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|151401377|gb|EV271191.1|EV271191
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTAAAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAA
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagcttga ... ctaaatgcagGTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAA
EST: gi|192321001|gb|FK013503.1|FK013503
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAA
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagcttga ... ctaaatgcagGTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAA
EST: gi|13482016|gb|BG511359.1|BG511359
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAA
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagcttga ... ctaaatgcagGTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAA
EST: gi|151404534|gb|EV274348.1|EV274348
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAA
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagcttga ... ctaaatgcagGTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgtttccttttctcgaccccctgggctttgattgagtcactaaatgcagGTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAAGAGCTTCAG
                                           cactaaa  putative branch site (score: 2)
                                tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaaacctttgttgtttgttggtaatgatggtaatcttttctattttttctgtttccttttctcgaccccctgggctttgattgagtcactaaatgcagGTTGCTAGAAATCTGGGAAAAACATTGCGTACATTTCAACCCACCATTAAAGAGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - -acctttg
- - - - - - -tgtttgt
- - - - - - - - - - - - - -gatggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggctttg