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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatctttgatttgaatatttcattatttattacattatgggtgcataatgtattttatttgtgttttgcttcaatggtatgcttccttattagtctc...

Basic information

species Glycine max
transcript GLYMA14G04410.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04410.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 5'ss of exon 3
TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatctttga----tttgaatatt--tcattatttattacatt---atgggtgcataatgtattttatttgtgttttgcttcaatggtatgcttccttattagtctc---
||| || |||||||||| ||| |||||||| || |||||||||||| ||||||||||||||||||||||||| ||||||||||||||  ||| |     ||  ||||   | | |||  |||   ||   |||  |  ||| | ||    |||     ||  ||||  ||  |||  |  | |||  ||     
TCAAGTGTACATGGCTAGAGAAATCAAAACAGGGGAAATTGTTGCTTTGAAGAAAATACGAATGGACAATGAAAGAGAGGGGgtataatttttaaacacttagatataaatgactataaattttgttggcatgtttttatattatagag-attcaaacttctcttc--tgaaatgtattttgatttttcatcag

upper sequence: GLYMA14G04410.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S3_535V6.1 (Physcomitrella patens), 5'ss of exon 2
TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatctttgatttgaatatttcattatttattacattatgggtgcataatgtattttatttgtgtttt-gcttcaatggtatgctt--ccttattagtctc-
 || || |||||||| || || |     || |||||| ||||||| ||||||||| | || ||||||||||||| ||| |||||||  |   |||||  ||  | | | |  |  || |     |||     | || || |||| || | |  |||   | | ||  | |   | ||||  | |  
GCAAGTGTACATGGCAAAGGATAAATCGACAGGTGAAGTTGTTGCGCTGAAGAAAGTTCGTATGGACAATGAGAAAGAAGGGgtatgac---gatttctatcgtacttaaggttgtagaagg-aggtagtggaggttttgtattggtttctgagctctgaagatactcataatcctattgctatta
















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|208125981|gb|GD921641.1|GD921641
EST:     GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG                         TTTCCTATAACTGC
genomic: GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatcttt ... gccattgcagTTTCCTATAACTGC
EST: gi|213617624|gb|DB969336.1|DB969336
EST:     GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG                         TTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
genomic: GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatcttt ... gccattgcagTTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
EST: gi|193350783|gb|FK314133.1|FK314133
EST:     GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG                         TTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
genomic: GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatcttt ... gccattgcagTTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
EST: gi|11275076|gb|BF325399.1|BF325399
EST:     GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG                         TTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
genomic: GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatcttt ... gccattgcagTTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
EST: gi|208052340|gb|GD855235.1|GD855235
EST:     GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG                         TTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
genomic: GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatcttt ... gccattgcagTTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
EST: gi|193694291|gb|FK630331.1|FK630331
EST:     GTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG                         TTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
genomic: GTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatcttt ... gccattgcagTTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
EST: gi|19348210|gb|BM892742.1|BM892742
EST:     GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGG                         TTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT
genomic: GTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatcttt ... gccattgcagTTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGGTTTACATGGCTAAAGAGATCAAAACTGGTGAAATTGTTGCTCTGAAGAAAATACGAATGGACAATGAGAGAGAGGGGgtatatctttgatttgaatatttcattatttattacattatgggtgcataatgtattttatttgtgttttgcttcaatggtatgcttccttattagtctc

- - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG