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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactctttactagtgttaactttctgtgcatattataactgttttttgtgctatatagatactctttgagtgctgaattgaggagatttttgtttctagGTTATTGTTTCTAGGATGAGATACATATCATCCCAAACAGAACGTGCAGTACGGTTTGTAGGTCTTTCTACAGCTCTGGCTAATGCTGG

Basic information

species Glycine max
transcript GLYMA06G21970.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G21970.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os03g11470.1 (Oryza sativa), 3'ss of exon 12
-----------------------------------------------------------------------------------------------ctactctttactagtgttaa--ctttctgtgcatattataactgttttttgtgctatatagatactctttgagtgctgaattgaggagatttttgtttctagGTTATTGTTTCTAGGATGAGATACATATCATCCCAAACAGAACGTGCAGTACGGTTTGTAGGTCTTTCTACAGCTCTGGCTAATGCTGG
                                                                                                |  |||  | |  | ||||  |  ||| | |||  | |   |||||||     |   ||  |  |     | || | |     |  |||||||  ||  |||| ||||| || || ||| ||||||||||||| |||||||||||| || | |||||||| ||| | || |||||  | || |||||| |
gtatcatttctggaagtcaaagacatgcaacacatgttatggtccataagtaacttcatttactttaactctatctcagggcaacataatttattgtcttctgcattcatcttaatcccatctattcatgctgtgcttgtttttcaaagt---tatctttttgccaattgttta-ccatgatgattttt--tttcagGTCATTGTATCAAGAATGCGATACATATCATCACAAACAGAACGTTCAATTCGGTTTGTTGGTTTATCAACAGCATTAGCCAATGCTCG

upper sequence: GLYMA06G21970.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv17s0000g07230.t01 (Vitis vinifera), 3'ss of exon 19
-----ctactct-ttactagtgttaactttctgtgcatattataactgttttttgtgctatatagatactctttgagtgctgaattgaggagatttttgtttctagGTTATTGTTTCTAGGATGAGATACATATCATCCCAAACAGAACGTGCAGTACGGTTTGTAGGTCTTTCTACAGCTCTGGCTAATGCTGG
     ||  | | ||| |  |  | | |||    || ||  |  ||||||||     || || |  ||||  |  |   |   |   | ||  | ||||  || ||||||||||||| |||||||||||||||||||| ||||||||  |  |||| ||||||||||| ||||| || ||| | || ||||| ||
taaagctgttatgttaatcatcctcattttagtagcctacaa--actgttttcataactgta-acttacttgtaaatctc---accaaagaactgtttgactccagGTTATTGTTTCAAGGATGAGATACATATCATCACAAACAGAGAGGACAGTGCGGTTTGTAGGACTTTCAACTGCTTTAGCAAATGCAGG
















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|18732355|gb|BM526990.1|BM526990
EST:     TATTGGATGAGATTCACTTATTGGGGGCTGATCGTGGACCCATTCTTGAG                         GTTATTGTTTCTAGGATGAGATACATATCATCCCAAACAGAACGTGCAGTA
genomic: TATTGGATGAGATTCACTTATTGGGGGCTGATCGTGGACCCATTCTTGAGgtatatgctt ... ttgtttctagGTTATTGTTTCTAGGATGAGATACATATCATCCCAAACAGAACGTGCAGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgctatatagatactctttgagtgctgaattgaggagatttttgtttctagGTTATTGTTTCTAGGATGAGATACATATCATCCCAAACAGAACGTGCAGTACGGTTTGTAGGTCTTTCTACAGCTCTGGCTAATGCTGG
                                          tttttgtttct  CT-rich tract
       tatatagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctactctttactagtgttaactttctgtgcatattataactgttttttgtgctatatagatactctttgagtgctgaattgaggagatttttgtttctagGTTATTGTTTCTAGGATGAGATACATATCATCCCAAACAGAACGTGCAGTACGGTTTGTAGGTCTTTCTACAGCTCTGGCTAATGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - ctttctg
- - - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - -tgctata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa