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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttgatattgctgcttgtggcaccatttggttgaatgattctcttgttttttataagctacatcaatgatgatacatatatatgtgctgccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAGAAGTTAACCGAAATGCTCACAGAGATGTGTGAGAACTACAACACTTTGC

Basic information

species Glycine max
transcript GLYMA15G00570.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G00570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 2
gatttgatattgctgcttgtggcaccatttggttgaatgattctcttgtttt-ttataagctacatcaatgatgatacatatatatgtgctgccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAGAAGTTAACCGAAATGCTCACAGAGATGTGTGAGAACTACAACACTTTGC---
    | | ||    | || |||    |        ||  | |   |    |  || |||      |   |  |||  |     |    | |  ||| |       ||||||   | | |||| || |||| |  ||||  |||||||||| |||| |||| |||||||| |||| |||||||||||| |||||| |||||    
----tcaaatcatagattatggaggaagaaaagaaaagaagttgttcacgtaattgtaattggggtggtttctgaagctgtgttccccgttttcatgtacacagACAGGTGTTCTTGTGGAGAAATTGAACCAAGTGAACGCAGAAAACAGGAAGCTAACGGAAATGCTAACAGTGATGTGTGAGAATTACAACGCTTTGAGAA
















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|120491123|gb|EH219290.1|EH219290
EST:     ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAG                         TCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
genomic: ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAGgttagttctg ... gccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
EST: gi|17153505|gb|BM143438.1|BM143438
EST:     ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAG                         TCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
genomic: ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAGgttagttctg ... gccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
EST: gi|17401736|gb|BM178518.1|BM178518
EST:     ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAG                         TCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
genomic: ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAGgttagttctg ... gccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
EST: gi|209698492|gb|BW652384.1|BW652384
EST:     ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAG                         TCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
genomic: ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAGgttagttctg ... gccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
EST: gi|209717341|gb|BW659044.1|BW659044
EST:     ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAG                         TCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG
genomic: ATTTTTTCTCATTGGATTTGGAGGTGAAGAAATCTTCTGTAAAACAAGAGgttagttctg ... gccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttttataagctacatcaatgatgatacatatatatgtgctgccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAGAAGTTAACCGAAATGCTCACAGAGATGTGTGAGAACTACAACACTTTGC
                                              ccatttc  CT-rich tract
                         atgatacatatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttgatattgctgcttgtggcaccatttggttgaatgattctcttgttttttataagctacatcaatgatgatacatatatatgtgctgccatttcagTCAGCAGGTGCCTTGGCGGAGGAACTGAAGCGGGTGAGTGCAGAAAACAAGAAGTTAACCGAAATGCTCACAGAGATGTGTGAGAACTACAACACTTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - -ttgctgc
- - - - - - - - ttgtggc
- - - - - - - - - - - - ccatttg
- - - - - - - - - - - - - - - - -tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtgc