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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttcaaatataagcttttgcttagtagtgtgcatgataaatgaatgggtcaaattttctagtcctctaaatgtcattttacttcattggcctgga...

Basic information

species Glycine max
transcript GLYMA08G09050.1
intron # 9
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09050.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os01g48270.1 (Oryza sativa), 5'ss of exon 9
GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttcaaatataagcttttgcttagtagtgtgcatgataaatga--atgggtcaaattttctagtcctctaaatgtcattttacttcattggcctgga
|||||| || || ||||||||||| || ||||||||| |||| || |||||| | || ||||||||||||||||| ||| | || ||| | ||||| || ||||||||       || |  |    || |    |   | |  | ||    |   |   | |   || |   | |  | |  | |||  | |    ||| | 
GGATGGGTTAACTAAGACAGATGATCTCGTTTTTGTTCTAGCCGCCACAAATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAACGTgtatccttttttctcaaaccatcttgtaatttctttgttcacgagtgctcctaaatactactccgtaattgcc-agttttgctattaggtaaactcccttg-

upper sequence: GLYMA08G09050.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G115766_T02 (Zea mays), 5'ss of exon 8
GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttcaa-atataagcttttgcttagtagtgtgcatgataaatgaatgggtcaaat-tttctagtcctctaaatgtcattttacttcattggcctgga
|||||| ||||| ||||||||||| || ||||||||| |||| ||||||||| | || |||||| |||||||||| ||||| || || || |||||||| ||||||||    | |||| ||| || ||   |   |   ||||  |  |||       || ||  |||   | |  ||    || ||  || |||  ||   
GGATGGGTTGACTAAGACAGATGAGCTTGTTTTTGTTCTAGCAGCAACAAATTTACCATGGGAATTGGATGCAGCAATGCTGCGTCGGCTGGAGAAGCGTgtatccttttctaaataatcttgtgtttcaaatcttagttgatttacaaatttcatgcatattgttagagatatgtatagacttgtatatctttgtactc--

upper sequence: GLYMA08G09050.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 9
GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttcaaatataagcttttgcttagtagtgtgcatgataaatgaatgggtcaaattttctagtcctctaaatgtcattttacttcattggcctgga
||||||||||||||||||| | ||  |||| |||||  | || || |||||||||||||||||| |||||||||||||||| || || ||||||||||| ||||   |   |  | |   ||| | |  |  | |      |  |  ||||| |  |   |   |   || |   ||||  | | | |||          
GGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctagtagttga---tttacattatcatata---agttgacaaatggattga---tctcacctctgtttgtgtctctgtccatcag---------

upper sequence: GLYMA08G09050.1 (Glycine max), 5'ss of exon 9
lower sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttcaaatataagcttttgcttagtagtgtgcatgataaatgaatgggtcaaattttctagtcctctaaatgtcattttact---tcattggcctgga
|||||| ||    || ||  |||| || || ||||||||||| ||||||||||| ||||||||||| |||||||| ||||| || ||||| ||||| |||||||||||             || |||| |    |  |  | |||||  ||  |||   |||    |  | ||    |||  |        |||| |      
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatcctt-------------ttacttactctcatagaacaaaaatgcttgtatcatgattttcttttgtttaggcctcaactagtgaaaccattag------

upper sequence: GLYMA08G09050.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 5'ss of exon 9
GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttcaaata--taagcttttgcttagt---agtgtgcatgataaatgaatgggtcaaattttctagtcctctaaatgtcattttacttcattggcctgga
|||||||||||||||||||||||| || |||||||||||||| ||||||||||| || |||||| |||||||||| ||||| || || ||||| ||| ||||||||||   ||   | |  |  | ||| ||   ||   ||||  | ||      |    ||  |||||||   ||| || | ||   |        |      
GGATGGTTTGACAAAGACAGATGAGCTTGTTTTTGTTTTAGCAGCAACAAATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGAGAgtatccttttgatgggtcaaatcatactttgtttcagatggcatttttaactttctgtcagaaagttctagtttactatatat-atgagagagagagagag----

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|209707326|gb|BW670618.1|BW670618
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|58024174|gb|CX710915.1|CX710915
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|58023441|gb|CX710182.1|CX710182
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|58024561|gb|CX711302.1|CX711302
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|298186847|gb|HO033946.1|HO033946
EST:     ATCTTCCTTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|58023989|gb|CX710730.1|CX710730
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|58018662|gb|CX705404.1|CX705404
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|10848344|gb|BF071723.1|BF071723
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTNCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|192331318|gb|FK021015.1|FK021015
EST:     ATCTTCCCTGGGAACTGGATGCAGTCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|58020971|gb|CX707713.1|CX707713
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|58021730|gb|CX708471.1|CX708471
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|22931036|gb|BU548175.1|BU548175
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
EST: gi|58021561|gb|CX708302.1|CX708302
EST:     ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGA                         ATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA
genomic: ATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttca ... taattgaaagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttcaaatataagcttttgcttagtagtgtgcatgataaatgaatgggtcaaattttctagtcctctaaatgtcattttacttcattggcctgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC