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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgatatacatatatatatatatatatgttccttaatttaattatatagtttgttcctttaactatatatataaagtttgattttgctaccacgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCCCTACAACGGTCCCAGAG

Basic information

species Glycine max
transcript GLYMA08G11120.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G11120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0010g03900.t01 (Vitis vinifera), 3'ss of exon 2
----------cgatatacatatatatatatatatatgttccttaatttaattatat-agtttgttcctttaactatatatataaagtttgattttgctaccacgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCCCTACAACGGTCCCAGAG
           ||| |   | |     || ||| || ||  |  |    ||| ||| |   ||    |  || || ||||||| | |||  | ||           | ||||||||||| ||||| ||||| || ||||| || || |||||||||||  |||||||||| ||||||||
aattataatttgattttttttttccagtacatagat-tttatagacactattgtattaagatgggattcgaaataaatatatatatttttttctta----------tgtagGAGTTAAGTAGTCAGCAGGAATATTTGAAACTTAAAGCACGTTATGAAGCCCTACAACGATCCCAGAG
















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|208102506|gb|GD900229.1|GD900229
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGGCC
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
EST: gi|207784105|gb|GD758415.1|GD758415
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGGCC
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
EST: gi|193388892|gb|FK353567.1|FK353567
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
EST: gi|207727051|gb|GD704277.1|GD704277
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGNGTCC
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
EST: gi|193345817|gb|FK311338.1|FK311338
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
EST: gi|193431784|gb|FK395584.1|FK395584
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
EST: gi|208046011|gb|GD848189.1|GD848189
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGGCC
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
EST: gi|193356941|gb|FK319605.1|FK319605
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATAGAGTA
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTAT-GAGT-
EST: gi|207756275|gb|GD727482.1|GD727482
EST:     AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTG                         GAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC
genomic: AATGTAACTATGGTGCGCCTGAGGCTAATGTGTCTACACGGGAAGCCTTGgtaatggtga ... acgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttgttcctttaactatatatataaagtttgattttgctaccacgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCCCTACAACGGTCCCAGAG
           tttaactatatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgatatacatatatatatatatatatgttccttaatttaattatatagtttgttcctttaactatatatataaagtttgattttgctaccacgattctagGAGTTAAGCAGTCAACAGGAGTACTTGAAGCTGAAGGCACGTTATGAGTCCCTACAACGGTCCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - gttcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctacc