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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAAGCTTACGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatatatagatatatattcaccaaaatgttaacaaattacacgaaaaaacgaaataacaaaaaaataaataaaaccctctttcttattatttttg...

Basic information

species Glycine max
transcript GLYMA08G11120.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G11120.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os08g41950.2 (Oryza sativa), 5'ss of exon 1
TGAAGAAAGCTTACGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatatatagatatatattc--accaaaatgttaa-caaattacacgaaaaaacgaaataacaaaaaaataaataaaaccctctttcttattatttttg
| ||||| || |||||||| ||||| || || || |||||||| || |||||||||||||||||  | || || || ||||||||||||||||     ||||  || |   |   ||  || ||  | | |    | || |  |   |||   | |    |||  |  ||   ||| ||   ||  | ||   |||   | | 
TCAAGAAGGCGTACGAGCTCTCCGTCCTCTGCGACGCCGAGGTCGCCCTCATCATCTTCTCCAACCGCGGCAAGCTCTACGAGTTCTGCAGCACCCAGAGgttcatttcatttcctagctactctaatccatccatcaaacccacatcacatcacacttcaatttcgcaagcttaattag--ccaccctttcgattggatct-

upper sequence: GLYMA08G11120.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os09g32948.1 (Oryza sativa), 5'ss of exon 1
TGAAGAAAGCTTACGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatatatagatatatattcaccaaaatgttaacaaattacacgaaaaaacgaaataacaaaaaaataaataaaaccctctttcttat-tatttttg
| ||||| || |||||||| ||||| || || || |||||||| || |||||||||||||||||  | || || || ||||||||||||||| |   |||||||||||| || ||   |  |   |       |  |     || |   | |   | |    |    ||   |   |       ||||||         ||
TCAAGAAGGCGTACGAGCTCTCCGTGCTCTGCGACGCCGAGGTCGCCCTCATCATCTTCTCCAACCGCGGCAAGCTCTACGAGTTCTGCAGCGGCCAAAGgtatatatacatggacgcac-tgggcgcgcgcctcgatctgctatagctagatcggtagctgcttgcaacgtagctagctagggtttcttgcgcgcgcctg

upper sequence: GLYMA08G11120.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os06g06750.1 (Oryza sativa), 5'ss of exon 1
TGAAGAAAGCTTACGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatatatagatatatattcaccaaaatgttaacaaattacacgaaaaaacgaaata-acaaaaaaataaa--taaaaccctctttcttattatttttg---
||||||| || |||||||| ||||| || || || |||||||| || ||||||||||||||||   | ||    || | |||||||| || |   ||  ||||      ||   ||| ||  || |    | | |  |        |  | ||   | ||| |        |||   |||  |    ||  ||| |   ||||   
TGAAGAAGGCGTACGAGCTGTCCGTGCTCTGCGACGCCGAGGTCGCCCTCATCATCTTCTCCACCCGCGGCCGCCTCTTCGAGTTCTCCACCTCCTCCTGgtac-----tactaata-attctctcttgcaagctctcgccccttgcagagaattcatatatatctcgccctaattctaatgcaaagttagttaattagtttgcag

upper sequence: GLYMA08G11120.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G129034_T02 (Zea mays), 5'ss of exon 1
TGAAGAAAGCTTACGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatatatagatatatattcaccaaaatgttaacaaat-tacacgaaaaaacgaaataacaaaaaaataaataaaaccctctttcttattatttttg-
| ||||| || |||||||| ||||| || || || ||||| || || |||||||||||||||||  | || || || ||||||||||||||| |    |||||||   |   |    | |    || |  | |    || || || |   |   || | ||   | |    |   |          ||      |       
TCAAGAAGGCGTACGAGCTCTCCGTGCTCTGCGACGCCGAAGTCGCGCTCATCATCTTCTCCAACCGCGGCAAGCTCTACGAGTTCTGCAGCGGACAGAGgtatacgcacgcatgcgtgtgcgaac-accacgcacgcacatatatatacatggac-acatggtacatgtgtgtgttctgtggcagttgccggaagccgcag

upper sequence: GLYMA08G11120.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G24260.1 (Arabidopsis thaliana), 5'ss of exon 1
TGAAGAAAGCTTACGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatata----tagatatatattcaccaaaatgttaacaaattacacgaaaaaacgaaataacaaaaaaataaataaaaccc-tctttcttattatttttg
|||||||||| ||||||||||| ||||| |||||||| || |||||||||||||||||||| ||||||||||| ||||||||||| ||||| ||||| |||||||||| ||    |  |||||||||    | ||  | ||||  ||| |   | | |  || ||||| ||||||   |   |    |   |||   | |     
TGAAGAAAGCATACGAGCTTTCAGTTCTATGTGATGCAGAAGTTGCTCTCATCATCTTCTCAAATAGAGGAAAGCTGTACGAGTTTTGCAGTAGTTCGAGgtatatatctacttttgtatatatattacttataacataaacattttatat--acatattaagtaacacaaaaatgtcttgtatgtatgggtctctctgtga---

upper sequence: GLYMA08G11120.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv01s0010g03900.t01 (Vitis vinifera), 5'ss of exon 1
TGAAGAAAGCTTACGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatatatagatatatattcaccaaaatgttaacaaattacacgaaaaaacgaaataacaaaaaaataaataaaaccctctttcttattatttttg
| ||||| || ||||| ||||| || || || || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| || || |||||   | | |   | | | |      ||||  | ||     ||||            |||||| ||||   ||   ||           ||| || |  
TCAAGAAGGCGTACGAACTTTCGGTGCTCTGCGACGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTCTACGAGTTCTGCAGTAGCTCGAGgtaataacacaggaaaagaaaaagtagaaaacctaaatttgatacaaacttgcttttcataacacaaaacacaaagcaagagaaaaggaaattgttctct

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|208279831|gb|GE078461.1|GE078461
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|208102506|gb|GD900229.1|GD900229
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|207784105|gb|GD758415.1|GD758415
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|193388892|gb|FK353567.1|FK353567
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTTACCTAGAAATGTAACTATGGTGCGCCT
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGG-TACC-AGAAATGTAACTATGGTGCGCCT
EST: gi|207727051|gb|GD704277.1|GD704277
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|208157311|gb|GD955913.1|GD955913
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAA
EST: gi|193345817|gb|FK311338.1|FK311338
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|193431784|gb|FK395584.1|FK395584
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|208046011|gb|GD848189.1|GD848189
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|193413126|gb|FK380861.1|FK380861
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATTGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTG
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCAT-GCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTG
EST: gi|208310841|gb|GE108105.1|GE108105
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|193451978|gb|FK420988.1|FK420988
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|193501099|gb|FK464616.1|FK464616
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|193356941|gb|FK319605.1|FK319605
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|193464580|gb|FK434146.1|FK434146
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
EST: gi|207756275|gb|GD727482.1|GD727482
EST:     ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAG                         CATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatat ... aaacgtgcagCATGCTCAAAACGCTAGAGAGGTACCAGAAATGTAACTATGGTGCGCCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAAGCTTACGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTGTACGAGTTCTGCAGCAGTTCAAGgtatatatatatagatatatattcaccaaaatgttaacaaattacacgaaaaaacgaaataacaaaaaaataaataaaaccctctttcttattatttttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctctt