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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGAAGGATGAAGGAAACAGTGATGTAGAAGATCTTGTGAATAGTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaaaaatattgttcccctccttcaagaaaataactgggtgggaagcagatgaatatagaggctgtaatcagagttgtaacttagcatctaatt...

Basic information

species Glycine max
transcript GLYMA20G31490.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31490.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G044681_T01 (Zea mays), 5'ss of exon 16
GGGGAAGGATGAAGGAAACAGTGATGTAGAAGATCTTGTGAATAGTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaaaaatattgttcccctccttcaagaaaataactgggtgggaagcagatgaatatagaggctgtaatcagagttgtaacttagcatctaatt-------------
|   || |||||  |||    |||  |   ||||||  ||| |  |||||| |||||||||| ||| ||||| || |||||||||||||||||||||       | | |   |||    | |  | | | |    ||  |    | |  ||| ||      | | |||  | | | || || |   || |||||             
GAATAATGATGAGCGAAGTTCTGACATGCGAGATCTGATGACTTCTTTCTCTGCGCTTGAAGAGAAAGTCCTGGACCAATATACTTTTGCAAAGgtat-----gatacacaattcagggcat--aggcatagtgttgattaaccaccgaatgcat------gatttaacaaaattggttacatcatatataattataaaagggtagg

upper sequence: GLYMA20G31490.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G050647_T01 (Zea mays), 5'ss of exon 16
GGGGAAGGATGAAGGAAACAGTGATGTAGAAGATCTTGTGAATAGTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaaaaatattgttcccctccttcaagaaaataactgggtgggaagcagatgaatatagaggctgtaatcagagttgtaactt-agcatctaatt---
|   || || ||  |||    |||  |   ||| ||   || |  |||||| || ||||||| ||| ||||| || |||||||||||||||||||||    | | |||   |  |      || |  ||    ||||  ||        |  || || ||   ||| ||     || ||||   || ||||   |   
GAATAATGAGGAGCGAAGTTCTGACATGCGAGACCTGAGGACTTCTTTCTCTGCACTTGAAGAGAAAGTCCTGGACCAATATACTTTTGCAAAGgtatgatgcacaattcaggacatagtgttgattaa--ctactgaatgcatgatttagcaaaattga--ttgtcatatatattataaccccagtatctttctttc

upper sequence: GLYMA20G31490.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 16
GGGGAAGGATGAAGGAAACAGTGATGTAGAAGATCTTGTGAATAGTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaaaaatattgttcccctccttcaagaaaataactgggtgggaagcagatgaatatagaggctgtaatcagagttgtaactt-agcatctaatt--
||  |  ||||||||| |||||||  ||  |||| | ||     ||||||| | |||||||| ||||||||||| ||| |||||||| |||||||||   |    ||| |  |||| |   ||    |||||           |  || ||| |  | ||  |     |  |  || |      || ||    ||  
GGAAAGAGATGAAGGAGACAGTGACATACGAGATTTAGTAGTGTGTTTCTCTGGGCTTGAAGAGAAGGTCCTTGCACAGTATACTTTCGCAAAGgtac--aactgaatgtgcttcctcaatttagttaaaatgttgctactcaacacacatgcaattggaaac-accttgggtattctggtcggaggattatgtttt

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|208071347|gb|GD872976.1|GD872976
EST:     GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAG                         GACAAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCA
genomic: GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaa ... ttctcatcagG-C-AAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCA
EST: gi|193451540|gb|FK417960.1|FK417960
EST:     GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAG                         GCAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCATT
genomic: GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaa ... ttctcatcagGCAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCATT
EST: gi|193682726|gb|FK623432.1|FK623432
EST:     GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAG                         GTCAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCAT
genomic: GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaa ... ttctcatcagG-CAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCAT
EST: gi|208167959|gb|GD966045.1|GD966045
EST:     GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAG                         GCAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCATT
genomic: GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaa ... ttctcatcagGCAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCATT
EST: gi|192303414|gb|FG995666.1|FG995666
EST:     GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAG                         GCAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCATT
genomic: GTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaa ... ttctcatcagGCAAACTTGATCAGATCTGCTGCCATGAATTATCTGCTGCATTCTGGCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGAAGGATGAAGGAAACAGTGATGTAGAAGATCTTGTGAATAGTTTCTCAGCGCTTGAAGGGAAGGTCCTTGAACAATATACTTTTGCAAAGgtaatgagaaaaatattgttcccctccttcaagaaaataactgggtgggaagcagatgaatatagaggctgtaatcagagttgtaacttagcatctaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtggg