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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagtcaagcatatgttagcttcttttatgtcttttgtcagttagttctaattccttgccaagatttaacattacagtcctggtccatttttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAATGGTCAGTATGAATGAGATGGCAGAGATTGTTCTTAGCTTTGAGGATAAG

Basic information

species Glycine max
transcript GLYMA19G43400.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 5
caagtcaagcatatgttagcttctt-ttatgtcttttgtcagttag--ttctaattc---cttgccaagatttaacatta--cagtcctggtccatttttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAATGGTCAGTATGAATGAGATGGCAGAGATTGTTCTTAGCTTTGAGGATAAG
           ||||  |||| ||| | |  |  ||    || |||    ||||  |   | ||   ||||   |   |   |     || | ||      | | ||| ||||| || || |||||||| ||||||||||| |||||||| ||||||||||| || ||||| |||||||| || ||  |||| ||||| ||||||| |
----------gtatgc-agctacttgtcacattattatctagatagaacactaaaccacacctgattagatgagaagctggtctaatatgatacaaaca-atttctagGTTGACAAAGTCGGACTTCCGTGAGCCAGTGAACATTGGAAGCGATGAAATGGTAAGCATGAACGAGATGGCTGAAATCATTCTCAGCTTCGAGGATAGG

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 5
-----------------------------caagtcaagcatatgttagcttcttttatgtcttttgtcagttagttctaattccttgccaagatttaacattacagtcctggtccatttttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAATGGTCAGTATGAATGAGATGGCAGAGATTGTTCTTAGCTTTGAGGATAAG
                              || | |||||   | |||||  |    ||| || |||     | |    | ||   | ||   | | ||  |   | ||    |  | |     |  |||||||| || ||||||||||| ||||||||||| || ||||| ||||| ||||| || ||||| |||||||| ||||| || ||  |||||||||||| |
gtatgtctgtgtgctttggatatactaccaaatttaagcaagagctagctgttgcc-tgtgttgtgtatagcaatggagaatc---gacattgtatgacgatgatgcccaca-ctgtgtgcac-tgcagATTGACCAAGTCAGACTTCCGCGAGCCAGTGAACATCGGAAGCGATGAGATGGTGAGCATGAACGAGATGGCTGAGATCGTGCTGGGCTTTGAGGATAGG

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 5
caagtcaagcatatgttagcttcttttatgtcttttgtcagttagttctaattccttgccaagatttaacattacagtcctggtccatttttgtgtt-tagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAATGGTCAGTATGAATGAGATGGCAGAGATTGTTCTTAGCTTTGAGGATAAG
              || ||  | | |  ||   ||  | |   |||| ||  |  | | |   |||      ||   || |    ||||||||| || ||| ||||| |||||||| ||||| ||||| ||||| || ||||| ||||| ||||| || |||||||||||||| ||||| ||||| ||||||||||| |||
--------------gtgagggtatctcctgatgttgatga---agttgta--tgttagacgtaattggctgatattttcgt----catttttgttttatagGTTGACAAAATCAGATTTCCGTGAGCCGGTGAACATCGGAAGCGATGAGATGGTGAGCATGAATGAGATGGCTGAGATGGTTCTCAGCTTTGAGGAAAAG

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|10256501|gb|BE824267.1|BE824267
EST:     ATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATNGACTAAATCAGACTTCCGGGAGCCAGTGAATATTNNNAGTGATGAAAT
genomic: ATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
EST: gi|7692518|gb|AW760622.1|AW760622
EST:     AGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: AGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
EST: gi|22928733|gb|BU545872.1|BU545872
EST:     CTTCATTGATGAGTGTGTTGAAGGTGTANNGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATANNNGAAGTGATGAAAT
genomic: CTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
EST: gi|298163054|gb|HO011787.1|HO011787
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
EST: gi|10255617|gb|BE823383.1|BE823383
EST:     CAAACAAGATNNNNNNNNNTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
EST: gi|192308376|gb|FK000900.1|FK000900
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
EST: gi|193360666|gb|FK325982.1|FK325982
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
EST: gi|192308771|gb|FK000119.1|FK000119
EST:     CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: CAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
EST: gi|193699315|gb|FK639420.1|FK639420
EST:     TAAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAG                         ATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT
genomic: -AAACAAGATCCTTCACCTTCATTGATGAGTGTGTTGAAGGTGTACTGAGgtattccttg ... ttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaattccttgccaagatttaacattacagtcctggtccatttttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAATGGTCAGTATGAATGAGATGGCAGAGATTGTTCTTAGCTTTGAGGATAAG
                                      tccattttt  CT-rich tract
               aagatttaacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagtcaagcatatgttagcttcttttatgtcttttgtcagttagttctaattccttgccaagatttaacattacagtcctggtccatttttgtgtttagATTGACTAAATCAGACTTCCGGGAGCCAGTGAATATTGGAAGTGATGAAATGGTCAGTATGAATGAGATGGCAGAGATTGTTCTTAGCTTTGAGGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - -caagcat
- - - - - - - - - gcttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggtcc