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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgattttttttactgttatgtatacttgaatttctcttctaaaaattagttattggcaattggatgtctattcatctactaaagcttgacataa...

Basic information

species Glycine max
transcript GLYMA02G03080.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 5'ss of exon 3
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgattttttttactgttatgtatact-tgaatttctcttctaaaaattagt-tattggcaattggatgtctattcatctactaaagcttgacataa-
|| |||||||||||||||||||| || ||||||||||| |||||||| ||| |||||||| |  | ||||||||  |||| ||| || |||  | | ||  || |  ||| || |  |       |    |   | | |  |   ||||   | |  | |  ||| |  ||| |   |   
GTCGATGGTATGGATGTTCTTGCAGTCAAACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagt-gaatttcctgattgccatttcgactgtgcacattatggacatttctggatctctcaggggttgggc-tgtgctgaaatac-actgctggtagtgtg

upper sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 3
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgatttttt----ttactgttatgtatacttgaatttctc--ttctaaaaattagttattggcaattggatgtctattcatctactaaagcttgacataa---
|||||||| ||||||||||||||||| || || || |||||||| ||||| || |||||| |    ||||| ||  ||||||||  | ||| |    ||| |  |||| ||||||   |  | |  || || | ||| | || ||    ||| |      | ||    || | | || ||||     
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaactttgtcgtgttaatagtatgcatacttatgtagcgcaattatatagatttgctactg----ttgaac-----tacagtggcttaggattcacatttctt

upper sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G027627_T01 (Zea mays), 5'ss of exon 3
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgattttttttactgttatgtatacttgaatttctcttctaaaaat---tagttattggcaattggatgtctattcatctactaaagcttgacataa
|| ||||| ||||||||||||||||| || ||||||||||||||||| || ||||||||  |  | ||||| ||  |||| |||  ||||     |   || ||  | ||   |||||  ||  |  |||   |   |||     |    ||      |||  ||        || |||| 
GTCGATGGAATGGATGTTCTTGCTGTGAAGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagt--atttaagaaataattctgatttctatcatttcagttacatgaatgcatgcatatcttagagcacataatccatcacgtatggggttatgccata-

upper sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G140150_T01 (Zea mays), 5'ss of exon 3
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagt--tgattttttttactgttatgtatacttgaatttctcttctaaaaattagttattggcaattggatgtctattcatctactaaagcttgacataa
|||||||| ||||||||||||||||| || ||||| |||||||||||||| || |||||| |    ||||| ||  ||||||||  |     | ||| |||   | | |  ||| ||    |   |  |    |  || |   ||  || |   |    | | |   ||    |  ||  
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAAGCGTGCAAATTTGCAAAAGATCATGCTGTTGCAAATGGCCCAATTgtgagtactatgaatcttttctgacttctgttattggatgcaccccatgtaggagaagtactattaa--ggcttgtttcgaagcaagggaaagaggggattg

upper sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G361693_T01 (Zea mays), 5'ss of exon 3
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagt--tgattttttttactgttatgtat-acttgaatttctcttctaaaaattagttattggcaa--ttggatgtctattcatctactaaagcttgacataa
|||||||| ||||||||||||||||| || ||||| |||||||||||||| || |||||| |    ||||| ||  |||| |||  |     | ||| |||   | | | | ||| || |  |   |  |   ||  || |   |    | |  ||    |   ||| |     |||      
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAAGCGTGCAAATTTGCAAAAGATCATGCTGTCGCAAATGGCCCAATTgtaagtactatgaatctttgctgacttctgttatttggatgtagcccatgtaggataactactattagggctcggagttggcttggctattctgtgttgc-----

upper sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 3
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgattttttt-tactgttatgtatacttgaatttctcttctaaaaattagttattggcaattggatg---tctattcatctacta-aagcttgacataa-
|| |||||||||||||   ||||||| |||||||||||||||||||| ||| | ||||| ||| |||| || ||  | || ||||  | ||||  || | | |    |  |||  ||| ||  ||     || ||  ||    ||  |  |   | | |  || | |||  |||   |  ||  
GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagtttgtattttagtattatcagacgt-tttgtttttttcccct-----ttggtccttactcatctggcgcattttgtaaatttgctatgagcaatatctagc

upper sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 5'ss of exon 3
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgattttttttactgtta------tgtatacttgaatttctcttctaaaaatta--gttattggcaattggatgtctattcatctactaaagcttgacataa
|| ||||||||||||||||||||||| ||||| || |||| |||||| ||||| |||||||| || ||||||||| |||| |||| | || |  | |||||       ||||| ||| ||  |  ||| |  ||| ||   || |||   ||| ||| |   |  |||| ||||  ||  |     
GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttacttatcctgctgtttccattttgtattcttaaaaattccttttgcaaactactattgttgttgattagatct---tctatcttctaattctgca-----

upper sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 5'ss of exon 3
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgattttttttactgttatgtatacttgaatttctcttctaaaaattagttattggcaattg-----gatgtctatt-catctactaaagcttgacataa--
|| ||||||||||||| |||||| || ||||| || |||| |||||| ||||| |||||||| || ||||||||| |||| |||| | || |  | |||||   || | ||     ||| ||||| ||| | ||| ||   || |      | |||  ||| |||||||||     | |       
GTAGATGGTATGGATGCTCTTGCGGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttacttatcctgctgtt---tacattt-----tctattctataaaattgttctttcaaactaccattgctgtagatttcatctactatcttctaattctgca

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|51338002|gb|CO981868.1|CO981868
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|254322999|gb|GR839912.1|GR839912
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|15664218|gb|BI701589.1|BI701589
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|58016185|gb|CX702927.1|CX702927
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTTTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|208280633|gb|GE080971.1|GE080971
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|15199292|gb|BI423757.1|BI423757
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|193721482|gb|FK662530.1|FK662530
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|58019317|gb|CX706059.1|CX706059
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|151406023|gb|EV275838.1|EV275838
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|19054086|gb|BM732753.1|BM732753
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|58016174|gb|CX702916.1|CX702916
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgattttttttactgttatgtatacttgaatttctcttctaaaaattagttattggcaattggatgtctattcatctactaaagcttgacataa

- - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA