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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttgtttttctttgttttaattattatttgcactcataatcatataaaaaattgaatgagtttctctaatctttgttttgtgttcaggtatatg...

Basic information

species Glycine max
transcript GLYMA19G04320.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G04320.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os08g41950.2 (Oryza sativa), 5'ss of exon 1
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttgtttt-tctttgttttaatt-attatttgcactcataatcatataaaa----aattgaatgagtttctctaatctttgttttgtgttcaggtatatg
||||||| || || ||||| || || ||||| || || ||||| ||||||||||||||||||| ||| |||||||| || || |||||||||||| | ||||   | |  |||  |   |  | ||||  ||   |   || || | ||| || | |    ||||     || ||   ||  |    ||| |   |  | | |   
TCAAGAAGGCGTACGAGCTCTCCGTCCTCTGCGACGCCGAGGTCGCCCTCATCATCTTCTCCAACCGCGGCAAGCTCTACGAGTTCTGCAGCACCCAGAGgttcatttcatttcctagctactctaatccatccatcaaacccaca-tcacatcacacttcaatttcgcaagcttaattagccaccctttcga--ttggatct---

upper sequence: GLYMA19G04320.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os09g32948.1 (Oryza sativa), 5'ss of exon 1
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgt----tgtttttctttgttttaattattatttgcactcataatcatataaaaaattgaatg-agtttctctaatctttgttttgtgttcaggtatatg
||||||| || || ||||| || || ||||| || || ||||| ||||||||||||||||||| ||| |||||||| || || |||||||||  | | |||||| | |     |     ||  |           || |||    |||   | ||    |  ||  || |   |  |||      ||||  ||  |  |  |   
TCAAGAAGGCGTACGAGCTCTCCGTGCTCTGCGACGCCGAGGTCGCCCTCATCATCTTCTCCAACCGCGGCAAGCTCTACGAGTTCTGCAGCGGCCAAAGgtatatatacatggacgcactgggcgcgcgcctcgatctgc---tatagctagatcggtagctgcttgcaacgtagctagctagggtttcttgcgcgcgcctg--

upper sequence: GLYMA19G04320.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os06g06750.1 (Oryza sativa), 5'ss of exon 1
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttgtttttctttgttttaattattatttgcactcataatcatataaaaaattgaatgagttt-ctctaatctttgttttgtgttcaggtatatg-
| ||||| || || ||||| || || ||||| || || ||||| ||||||||||||||||||||||| |||   || |  || |||| || | ||  | ||||    |  |  |||| | ||  ||    | |   | ||   |   |  | | | ||     |   |   ||||||      || ||      || |    
TGAAGAAGGCGTACGAGCTGTCCGTGCTCTGCGACGCCGAGGTCGCCCTCATCATCTTCTCCACCCGCGGCCGCCTCTTCGAGTTCTCCACCTCCTCCTGgtactactaataattctctcttgcaa--gctctcgccccttgcagagaattcatatatatctcgccctaattctaatgcaaagttagttaattagtttgcag

upper sequence: GLYMA19G04320.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G159397_T01 (Zea mays), 5'ss of exon 1
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgt-tgtttttctttgttttaattattatttgcactcataatcatataaaaaattgaatgagtttctctaatctttgttttgtgttcaggtatatg--
||||||| || || ||||| || || ||||| || || ||||| || |||||||||||||||| ||| |||||||| || || |||| ||||||  | ||||||      |        |||  ||  || ||   |    | |   |        |  |    |         | |  |      | | |   ||   |   
TCAAGAAGGCGTACGAGCTCTCGGTGCTCTGCGACGCCGAGGTCGCGCTCATCATCTTCTCCAACCGCGGCAAGCTCTACGAGTTCTCCAGCACGCAGAGgtatacacgcgcgcgcgcatgtacta-ctactacccggcagcgtgcccgcg--gtcaccttgccgctgccgggcagtggtcacacggcgctggagtgccttgg

upper sequence: GLYMA19G04320.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G129034_T02 (Zea mays), 5'ss of exon 1
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttgtttttctttgttttaattattatttgcactcataatcatata-aaaaattgaatgagtttctctaatctttgttttgtgttcaggtatatg-
||||||| || || ||||| || || ||||| || || || || || |||||||||||||||| ||| |||||||| || || |||||||||    | ||||||  |       |   |||   ||  |  |    | | ||||   ||| |   | |     |   | | | |  ||| ||     ||             
TCAAGAAGGCGTACGAGCTCTCCGTGCTCTGCGACGCCGAAGTCGCGCTCATCATCTTCTCCAACCGCGGCAAGCTCTACGAGTTCTGCAGCGGACAGAGgtatacgc-acgcatgcgtgtgcgaac-accacgcacgcacatatatatacatggacacatggtacatgtgtgtgttctgtggcagttgccggaagccgcag

upper sequence: GLYMA19G04320.1 (Glycine max), 5'ss of exon 1
lower sequence: AT5G15800.1 (Arabidopsis thaliana), 5'ss of exon 1
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtg-ttgtttttctttgttttaattattatttgcactcataatcatataaaaaattgaatgagtttctctaatctttgttttgtgttcaggtatatg
| |||||||| |||||  | |||||||||||||||||||| ||||| |||||||||||||||| |||||| ||||| ||||| || |||||| ||   | |||      | | |  || | | | | ||  |   |  | |  |    | ||   |  ||  ||   | |||| |    ||||| | | |  |   | | |
TGAAGAAAGCTTATGAATTGTCTGTTCTCTGTGATGCTGAAGTTGCTCTCATCATCTTCTCCAACCGTGGAAAGCTCTATGAGTTTTGCAGCTCCTCAAAgtaaacaactctctcactctttatcagtttcttgattgagtttttgctagatctgagcttagatctttgtctcaaggacttgttatatatagat-cacacg

upper sequence: GLYMA19G04320.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G02310.1 (Arabidopsis thaliana), 5'ss of exon 1
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttgtttttctttgtttta----attattatttgcactcataatcatataaaaaattgaatgagtttctctaatctttgttttgtgttcaggtatatg
| || ||||| |||||||||||||||||||| |||||||| ||  | |||||| ||||||||| |||||||||||| || || ||||||||||||  || |||  | |  || ||  |    |||    ||   | | |  |    | ||  |   |    |   ||||||||      ||||  ||   | || |   |    
TGAAAAAAGCTTATGAGCTTTCTGTTCTCTGCGATGCTGAAGTCTCTCTCATCGTCTTCTCCAACCGTGGCAAGCTCTACGAGTTCTGCAGCACCTCCAAgtacttctctttctttatacacttattagatctgtgtgtagatctttcatttttctagtcttgtgatgagttttatctttcttgattgctttttaacaaa----

upper sequence: GLYMA19G04320.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv14s0083g01050.t01 (Vitis vinifera), 5'ss of exon 1
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgta-tgtgttgtttttctttgttttaattattatttgcactcataatcatataaaaaattgaatgagtttctctaatctttgttttgtgttcaggtatatg
|||||||||| |||||||| || || || |||||||||||||| || ||||||||||||||||||||||| ||||| ||||| |||||||||| |   ||||  | | ||   || || | ||   ||   ||     | ||| || |  ||       | | ||  | | | | || | |   || | ||  | |   | 
TCAAGAAAGCTTATGAGCTCTCAGTCCTTTGTGATGCTGAGGTCGCTCTCATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAGgtcctctctttgattcctcttttcctatatctacgcatattcacaaacgcatgtcttcat-attggatctgtttgatttcttgattttatttggttgattt

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|193552203|gb|FK508960.1|FK508960
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193426151|gb|FK390858.1|FK390858
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193379080|gb|FK344414.1|FK344414
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACT
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACT
EST: gi|193428351|gb|FK395441.1|FK395441
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193343599|gb|FK306963.1|FK306963
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGT
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGG-
EST: gi|208171464|gb|GD971889.1|GD971889
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193440011|gb|FK408146.1|FK408146
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTG
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTG
EST: gi|207806384|gb|GD777391.1|GD777391
EST:     GAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: GAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|208044345|gb|GD839299.1|GD839299
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|208282760|gb|GE074670.1|GE074670
EST:     TGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: TGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193347274|gb|FK313048.1|FK313048
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|207744988|gb|GD716784.1|GD716784
EST:     ATCATCTTCTCCACCCGTGGTAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|208217948|gb|GE016526.1|GE016526
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACA
EST: gi|193422347|gb|FK391528.1|FK391528
EST:     ATCATCTTCTCTACCCGCGGCAAGCTTTATGAATTCTGTAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTTGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193397257|gb|FK363319.1|FK363319
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193328962|gb|FK295206.1|FK295206
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193633969|gb|FK581091.1|FK581091
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|207769754|gb|GD741312.1|GD741312
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193325247|gb|FK291441.1|FK291441
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|193402516|gb|FK365578.1|FK365578
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACNCTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|208071166|gb|GD868441.1|GD868441
EST:     TGAATTCTGCAGCACCAACAG                         CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
genomic: TGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGA
EST: gi|207705541|gb|GD689435.1|GD689435
EST:     ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAG                         CATGCTCAAAACNCTTGAAAGGTACCAAA
genomic: ATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttg ... gaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGAAAGCCTATGAGCTTTCTGTTCTCTGTGATGCTGAGGTTGCCCTCATCATCTTCTCCACCCGTGGCAAGCTTTATGAATTCTGCAGCACCAACAGgtatgtgttgtttttctttgttttaattattatttgcactcataatcatataaaaaattgaatgagtttctctaatctttgttttgtgttcaggtatatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaaa