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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAGCAATGGCAGAACAAAACCAAAACCAGACAACTGAAGCTGGAAGGCACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccaccccaattacattcctttgttaaaaaagaaaaaaaaaatctttttttcttttggtttttattttattttatataatagttatgttgaaaacaaaaatctttttttttcgggggggtgtttgataaaatggttatgttgtgtttag

Basic information

species Glycine max
transcript GLYMA02G11530.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G11530.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 5'ss of exon 1
TATAGCAATGGCAGAAC----AAAACCAAAACCAGACAACTGAAGCTGGAAGGCACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccaccccaattacattcctttgttaaaaaagaaaaaaaaaatctttttttcttttggtttttattttattttatataatagttatgttgaaaacaaaaatctttttttttcgggggggtgtttgataaaatggttatgttgtgtttag
   || ||  | ||| |     |||     || |  |||  |||||||| |||||||| ||||||||||||||||||||| | ||||||||||||||||| ||||||    |   ||    | || | |       |  |         |||||  ||| |   || |  || | |  | | |  |  |  ||||| |                                                         
--AAGGAACAGAAGATCTCTAGAAATGGCCACGAAGCAA--GAAGCTGGGAGGCACCAGGAGGTTGGCCACAAGAGCCTTTTGCAGAGTGATGCTCTTTATCAGgtaagctcttcat----tcccctcgaggcttcatcagtcttcgtccttttaatctgtattttctcgttctctgatttttcttcttcttgttgcag--------------------------------------------------------
















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|13481062|gb|BG510405.1|BG510405
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|19936522|gb|BQ080903.1|BQ080903
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|308098994|gb|HO760835.1|HO760835
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|19935964|gb|BQ080661.1|BQ080661
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|192325510|gb|FK018421.1|FK018421
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|26047747|gb|CA784441.1|CA784441
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCACAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|7591492|gb|AW707224.1|AW707224
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|192333796|gb|FK025841.1|FK025841
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|17401035|gb|BM177817.1|BM177817
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|15201563|gb|BI424930.1|BI424930
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|19936001|gb|BQ080677.1|BQ080677
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|192294152|gb|FG986241.1|FG986241
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGGTGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|7588790|gb|AW704578.1|AW704578
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|5677754|gb|AI938893.1|AI938893
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|21601527|gb|BQ611858.1|BQ611858
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAATAT
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|151393914|gb|EV263785.1|EV263785
EST:     GCCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|192325368|gb|FK018354.1|FK018354
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATACTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|23733582|gb|BU764995.1|BU764995
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|17402133|gb|BM178915.1|BM178915
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|16346918|gb|BI972513.1|BI972513
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
EST: gi|192304327|gb|FG996453.1|FG996453
EST:     ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAG                         TATATTCTGGAGGCCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA
genomic: ACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccacccc ... ttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAGCAATGGCAGAACAAAACCAAAACCAGACAACTGAAGCTGGAAGGCACCAAGAGGTTGGCCACAAGAGCCTTCTCCAGAGTGATGCTCTTTACCAGgtaccaccccaattacattcctttgttaaaaaagaaaaaaaaaatctttttttcttttggtttttattttattttatataatagttatgttgaaaacaaaaatctttttttttcgggggggtgtttgataaaatggttatgttgtgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG