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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtgttctttctttagttttgtttttgtttt...

Basic information

species Glycine max
transcript GLYMA13G19280.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 5'ss of exon 3
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtgttctttctttagttttgtttttgtttt--
 || ||||||||||||||||| |||||||| |||||||| || ||  ||||||||||||||||||| || ||||| ||||| ||| | |||||||||||||||   ||   | | | | |   || | | ||      ||  ||  ||    ||||   | | ||| || ||    | || | | | ||||   |  |    
CATCGAAAGTCTTGATCCAGCATTGCTACGCCCTGGTCGCATAGATCGGAAGATAGAATTTCCTCTGCCAGATATTAAAACTAGGCGGCGCATCTTCCAGgtaaatatccattagtatcttttagaacttca---gaatgcatgataa---ctgataagcagttcctttggt----tctcatgaatgttgtgaatcgtgcag

upper sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 4
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtgttctttctttagttttgtttttgtttt
 |||||||||||||| ||||||||||| ||||||||||| || ||||| ||||| ||||||||  | || ||||| ||||| ||||| || |||||||||||     |    ||| ||   |   |          ||| ||   | || | ||    | | || | | |   |  ||| ||  ||   |          
CATTGAAAGTCTTGACCCAGCTTTGCTTCGACCTGGTCGGATAGACAGAAAGATTGAATTTCCGTTACCAGATATTAAAACCAGGAGGCGGATCTTCCAGgtgcttttctacaatgtttcaagttc----------tgtcttattggaaacctg----cttcgttcttatcaatagttt-ttgggtgcag----------

upper sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtgttctttctttagttttgtttttgtttt---
 |||||||||||||||||||| ||||| || || |||||||||||||| ||||| ||||| ||| | |||||| |||| || ||| | ||||||||||||||     |     || |  |||||||     |  | |||  ||   |    |  |  || || |       |||| || |   | |||||||||  |      
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttct-----atgtgatgaaagcttctgagtcctgttcttttaa---ttaaaaagcatgatt------tgttgttaccaaaattttgttttgatgagcag

upper sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 3
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtgttctttctttag----ttttgtttttgtttt-
 |||||||||||||||||||| ||||| || || || || || ||| ||||||| ||||||||||| || ||||| ||||| ||  |||||||||||||||||    ||||      | || ||   |||        | ||||    | |   |||  ||        | |||||||  | |||    || |    ||||    
CATTGAAAGTCTTGATCCAGCCTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTTCCTCTACCAGATATTAAAACTAGACGACGCATCTTCCAGgtac-tgtgacg-----tctgtaaatgata-------atatttgcattaac--aatgttcttaataccctttgttcttattatagaaggttgtaaacttgtgcag

upper sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 3
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccat-----gtgtttgggaaagcttgatggcctggtccatttgtgttctttctttagttttgtttttgtttt
 ||||||||||||||||| |||||||| || || || || || ||| ||||||| ||||| ||||| || ||||| ||||| || ||||||||||||||||| |   | ||  || |   || || ||||    |||      |||| |  | | |||  || |||  |  ||    ||| |       |               
CATTGAAAGTCTTGATCCTGCTTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgt-gctgtaac--atctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttata-atgaaggttgtaaaccgtgcag------------

upper sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtg--ttctttctttagttttgtttttgtttt
||| || |||||||| |||||  |||| |||||||| || ||||| ||||| || || || ||||| || |||||||||||||| ||||| ||||||||||||   ||   ||||| |    |      | | | |||  ||     || |||  | |     |    |||||  |||| | | ||   | |          
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgta---atatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatag----------

upper sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 5'ss of exon 4
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtgttctttctttagttttgtttttgtttt
 || || |||||||| || ||  | ||  |||| || || || |||||||| || ||||| |||||||| |||||||||||||| ||||| |||||||||||   ||  |||  |  |    |||        |  | | |||  |  |  ||  | |   | ||   | | ||| ||  ||   |    || ||     
GATCGAGAGTCTTGACCCGGCACTTCTTAGACCAGGCCGGATCGACAGGAAAATCGAATTCCCTCTTCCAGATATCAAAACAAGAAGACGTATCTTCCAGgttc-cacaactggtgatccttaagt----tttctttctttttttgtgaattttctagaaagatctgatcg-gtttttaattgcatgccattattag---

upper sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgact----aattttgtgaaagcaata-------------cacccatgtgtttgggaaagcttgatggcctggtcca-tttgtgttctttctttagttttgtttttgtttt-----------
|||||||||| | |||||||||||||| || ||||||||||| || |||||||| ||||| ||||||||||| || |||||||| |||||||| |||||||||    ||  |     ||| ||  || ||||||             || ||   |  ||| || | ||  ||  ||    |    |||  | || |   ||      | |   || |           
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag

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|16349378|gb|BI974973.1|BI974973
EST:     AGACGCATCTTCCAG                         ATACACACGTCAAGGATAACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|193424245|gb|FK386832.1|FK386832
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|208151346|gb|GD948997.1|GD948997
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGA
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGA
EST: gi|207729139|gb|GD704907.1|GD704907
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGAATGACATTAGCTGATGA
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGA
EST: gi|15337660|gb|BI498316.1|BI498316
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|27424837|gb|CA936357.1|CA936357
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|208049577|gb|GD849362.1|GD849362
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|193721867|gb|FK662887.1|FK662887
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|209715036|gb|BW650887.1|BW650887
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|254325091|gb|GR834516.1|GR834516
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|208137422|gb|GD937988.1|GD937988
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|193535002|gb|FK493058.1|FK493058
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|21639088|gb|BM140134.1|BM140134
EST:     TCCTCTTCCTGATATCAAAACAAGGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: TCCTCTTCCTGATATCAAAACAA-GGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|193721078|gb|FK660320.1|FK660320
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|58017107|gb|CX703849.1|CX703849
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACATCGAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|207751706|gb|GD723615.1|GD723615
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|208152513|gb|GD949114.1|GD949114
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|31459887|gb|CD401915.1|CD401915
EST:     GATAGAATTTCCTCTTCCTGATATCGATACATAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: GATAGAATTTCCTCTTCCTGATATCAAAACA-AGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|33388030|gb|CA851237.1|CA851237
EST:     AATTTCCTCTTCCTGNATATCAAAACAAGGNAGNACGCATCTTCCAG                         N
genomic: AATTTCCTCTTCCTG-ATATCAAAACAAGG-AG-ACGCATCTTCCAGgtaggcatga ... tggaattaag-
EST: gi|33388030|gb|CA851237.1|CA851237
EST:     AATTTCCTCTTCCTGNATATCAAAACAAGGNAGNACGCATCTTCCAG                         N
genomic: AATTTCCTCTTCCTG-ATATCAAAACAAGG-AG-ACGCATCTTCCAGgtaggcatga ... tggaattaag-
EST: gi|6846539|gb|AW348829.1|AW348829
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGTAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
EST: gi|31460408|gb|CD402376.1|CD402376
EST:     AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAG                         ATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT
genomic: AGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatga ... tggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtgttctttctttagttttgtttttgtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA