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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcatgccattttaagtttatgcactaaaagttattttatattatttggttattttcatctctttttggtcaaattttattctcctaccataagt...

Basic information

species Glycine max
transcript GLYMA01G25940.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcatgccattttaagtttatgcactaaaagttattttatattatttggttattttcatctctttttggtcaaattttattctcctaccataagt
 |||||||| ||||||||||||||||||||  |||||||  |||| ||||||||||| ||||||||   |||  ||| ||  ||||  |    | |||   ||  || || | ||  | |||       | | |||| |                        
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatt-gcaacccacttgtagttgcttagtttaaaac-atcctaaat-agttactaattggttctgcatcttggacttgcag------------------

upper sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 10
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtagga---gcatgccattttaagtttatgcactaaaagttattttatattatttggttattttcatctctttttggtcaaattttattctcctaccataagt
 |||||||| ||||||||||||||||||||  |||||||  |||| ||||||||||| ||||||||      |||| ||  ||  | ||  |    | | |  |||  || || | ||  | |||     |   | |||| |                        
ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatcgctcgcatccctgttgtacttgcttagtttagaaatatcctaaat-agttaataattggttccggatcttggacttgcag------------------

upper sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 10
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcatgccattttaagtttatgcactaaaagttattttatattatttggttattttcatctctttttggtcaaattttattctcctaccataagt
 |||||||| |||||||| |||||||||||  |||||||  |||| ||||||||||| ||||||||   |||  ||| ||  ||||  |    | |||   ||  || || | ||  | |||       | | |||| |                        
ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatt-gcaacccacttgtagttgcttagtttaaaac-atcctaaat-agttactaattggttctgcatcttggacttgcag------------------

upper sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM5G850355_T04 (Zea mays), 5'ss of exon 9
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcatgccattttaagtt-tatgcactaaaagttattttatattatttggttattttcatctctttttggt-caaattttattctcctaccataagt
 |||||||| |||||||| |||||||||||  |||||||  |||| ||||||||||| ||||||||   |||  ||| ||  ||||   |    |||||  |  |  ||| |   |  ||  ||     ||||     | || || | |    |  |        
ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatt-gcaacccacttgtagttgcttagtttaaaacatcctaaatagttactaattggttctgcatcttggacttgcagatatgaggggcaaatttcctc-

upper sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 9
lower sequence: AT1G79210.1 (Arabidopsis thaliana), 5'ss of exon 10
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcatgccattttaagtttatgcactaaaagttattttatattatttggttattttc--atctctttttggtcaa--attttattctcctaccataagt
||||||||| |||||||| |||||||||||  | |||||  |||||||||| |||||||||||||  |       ||||||          || |||| ||| ||||  ||||||    | ||    || |||     | | |  |  |   | || |  || |   
GTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGGgtgag-------catttt---------taccaaaacttaatttactttatttccagagttcagaatttctcaaaagcctataacctccgtgtcttttcacag--

upper sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 9
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcatgccattttaagtttatgcactaaaagttattttat-attatttggttattttcatctctttt-tggtcaaattttattctcctaccataagt-
|||||| ||||||||||| ||||||||||| ||||||||| | || |||||  | ||||| |||||   ||||   |   |   ||| |    ||||  | |  | |  | | ||||   | | |||         |    ||  |||   ||  | |  |   | 
GTACACTGATGATATGGAACTTGATGATGCTGTCCACACAGCTATTTTGACACTCAAGGAGGGgtatatgcatcttaaacttcttttcttt--taaatttcagctaacgaatgtttgaaaactatcaaaaggcacatcaagaagctttgaacttat-ctgttgttc

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|120495257|gb|EH223424.1|EH223424
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|31560932|gb|CD486770.1|CD486770
EST:     CTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: CTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|213592922|gb|DB966027.1|DB966027
EST:     TGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: TGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|192309681|gb|FG999894.1|FG999894
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|31305572|gb|CD390775.1|CD390775
EST:     CTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: CTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|58014614|gb|CX701356.1|CX701356
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|192325446|gb|FK018387.1|FK018387
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|120494647|gb|EH222814.1|EH222814
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTT-GAGGGACAGATCTCAGGAAAAAA
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAA
EST: gi|57575724|gb|CX548699.1|CX548699
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|31472270|gb|CD414298.1|CD414298
EST:     CTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: CTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|8403449|gb|BE059083.1|BE059083
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTNTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|192316847|gb|FK010834.1|FK010834
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATTTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|19348090|gb|BM892622.1|BM892622
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|193720646|gb|FK662002.1|FK662002
EST:     GCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
genomic: GCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC
EST: gi|151406778|gb|EV276593.1|EV276593
EST:     ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAG-AAAAAACATTGAAATTGGCATAATCGGTGC
genomic: ATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcat ... tgtttcacagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATCGGTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcatgccattttaagtttatgcactaaaagttattttatattatttggttattttcatctctttttggtcaaattttattctcctaccataagt

- - - - - - -  GGAGCT
- - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA