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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttttcctggttatctttcatccttcttgtgttttgtgagtgttttgtcattgttttcaacttatggcacag

Basic information

species Glycine max
transcript GLYMA11G11510.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11510.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 5'ss of exon 3
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttttcctggttatctttcatccttcttgtgttttgtgagtgttttgtcattgttttcaacttatggcacag---------------------------------------------------------------------------------------------------------------------
|| || ||||||||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||| |||||   |         | |  ||  ||     |||   | ||||    ||  ||||   ||| | |||   ||    | |                                                                                                                      
GATTATGTGCCAACTGTATTTGACAATTTCAGTGCAAATGTTGTGGTGGATGGGAGCACTGTTAATCTAGGGTTGTGGGATACTGCAGgtaaagttccagacctgtaggaattgtttg---ttcacatttttttgaggtactttgc--ttgctctcagggtaaaaaatacattgttcttaaaggcaaacaaaaactactttaaagatgctgtctcaatggttgtcttaccactacacctctttgagggttcttaatattgaactgattttgttaatttatggaacag

upper sequence: GLYMA11G11510.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 5'ss of exon 3
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtat--agtttttcctgg---ttatctttcatccttcttgtgttttgtgagtgttttgtcattgtt--ttcaactta---tggcacag--------
|| ||||| ||||| || |||||||||||||| ||||||||||| || ||||||| ||| || ||||| || || |||||||| || ||||||      | ||   || |    | || ||  | | | ||||| ||  ||   |  |      || |  ||||  |||   | | || |        
GATTACGTACCAACCGTGTTTGACAATTTCAGCGCAAATGTCGTGGTCGATGGAAACACAGTCAATCTCGGATTATGGGATACAGCAGgtaagagacaggattcgactagaatctctcctttgtacctattgtggttactgtcgggatcacgggtgctgattcacattaatttaggacgggcgctgca

upper sequence: GLYMA11G11510.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ04304 (Selaginella moellendorffii), 5'ss of exon 2
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttttcctggttatctttcatccttcttgtgttttgtgagtgttttgtcattgttttcaacttatggcacag
||||||||||| || |||||||| || || ||||| ||||| || |||||||| | |||||||||| | ||  | ||||| || ||||||| || |||      ||||  |   |       |  |         |  || ||  |  ||||||       ||  | |||
GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttag------ctggaaaaactcggcttgttctaacgcaaacgcatgcttgctttttgtttctcgtaaatctcgcag

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|7589435|gb|AW705209.1|AW705209
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|298169211|gb|HO020571.1|HO020571
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGGGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|298197330|gb|HO044809.1|HO044809
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|298171990|gb|HO021582.1|HO021582
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|16996922|gb|BM086294.1|BM086294
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|5760314|gb|AI965741.1|AI965741
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|151394170|gb|EV264041.1|EV264041
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|19346953|gb|BM891833.1|BM891833
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|298177328|gb|HO027109.1|HO027109
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|26058249|gb|CA801163.1|CA801163
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|5342846|gb|AI795130.1|AI795130
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|23725796|gb|BU760863.1|BU760863
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|298182534|gb|HO031269.1|HO031269
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|4293505|gb|AI442057.1|AI442057
EST:     TGTCGGTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|192329017|gb|FK021091.1|FK021091
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|192297529|gb|FG989535.1|FG989535
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|7589250|gb|AW705028.1|AW705028
EST:     TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|192329018|gb|FK021092.1|FK021092
EST:     TGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGGGTTGTGGGATACTGCTGgtaagtatag ... tatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttttcctggttatctttcatccttcttgtgttttgtgagtgttttgtcattgttttcaacttatggcacag

- - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG