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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaatggattctgtgttaacatgtgtctttattaaaaaggaagagagaattctggttttttatagttttgtgatactcttacatgggctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG

Basic information

species Glycine max
transcript GLYMA18G53880.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G53880.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
---tctaatggattctgtgttaacatgtgtctt-tattaaaaaggaagagagaattctggttttttatagttttgtgatactcttacatgggctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG---
        || ||  |  ||||  || |||| | ||  | | |          ||| ||   | ||||||| ||  ||||   ||  ||   | | ||    |||||||||| ||||| ||  ||||   |||||||||||| ||||| || ||| | |||||| | |||||||| ||||| || ||||||||||| || ||||   
ttgatatgtgtatcttcagttag-atctgtcctgtaagatataccttttatctattatgaagtgttatagtgtta-gatatgattctatc--catactgcacagGTTGCTCGTGGTGATAACTCTGG---GGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG

upper sequence: GLYMA18G53880.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
tctaatggattctgtgttaacatgtgtctttattaaaaaggaagagagaattctggttttttatagttttgtgatactcttacatggg----ctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG
   |||  | | ||  |     |   |  | || |   || ||  ||     |  |        ||       ||| |||||  ||      | |||||| |||||||| | ||| ||||       ||||||  | ||||| |||||  | ||  |||||||  | |||||||| ||||| ||||||||||||||||| ||||
-tcaata-actttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagcc--agtatattcttatttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG

upper sequence: GLYMA18G53880.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
tctaatggattctgtgttaacatgtgtctttattaaaaaggaagagaga-attctggttttttatagttttgtgatactcttacatgggctttcttttt----------agGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG
            | | ||||||  | |   |    ||    ||   | | |||  | ||    | | ||     |   |||   ||| | | |||| ||          |||||||||| ||||||||   |||||| ||| | ||||| ||||| |||||| |||||||| | |||||||| ||||| |||||||| |||||||| ||||
-----------ttctattaacacctataaattcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG

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|208156859|gb|GD956315.1|GD956315
EST:     TTTGGGTATTCATATCTCCAGTGATTTTCCATGAGAGTGTTATGATTGCA                         GTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGA
genomic: TTTGGGTATTCATATCTCCAGTGATTTTCCATGAGAGTGTTATGATTGCAgtaagtattt ... ttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGA
EST: gi|16342803|gb|BI968398.1|BI968398
EST:     GGGTATTCATATCTCCAGTGANNNNNCATGAGAGTGTTATGATNNCA                         GTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTNNNGAGA
genomic: GGGTATTCATATCTCCAGTGATTTTCCATGAGAGTGTTATGATTGCAgtaagtattt ... ttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGA
EST: gi|51335619|gb|CO979485.1|CO979485
EST:     TTTGGGTATTCATATCTCCAGTGATTTTCCATGAGAGTGTTATGATTGCA                         GTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGA
genomic: TTTGGGTATTCATATCTCCAGTGATTTTCCATGAGAGTGTTATGATTGCAgtaagtattt ... ttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaattctggttttttatagttttgtgatactcttacatgggctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG
                               ctcttac  putative branch site (score: 3)
                                           ctttcttttt  putative PPT
           ttttttatagttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaatggattctgtgttaacatgtgtctttattaaaaaggaagagagaattctggttttttatagttttgtgatactcttacatgggctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG

- - - -gattctg
- - - - - - - - - -acatgtg
- - - - - - - - - - - - - - - -attaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - -attctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatggg