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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctactgacttctccctaactgcctaacgcatctctaatcatctgttctgcttcttgagactgggagatggtagttgcatatatcacgaggagat...

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 4
GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctactgacttctccctaactgcctaacgcatctctaatcatctgttctgcttcttgagactgggagatggtagttgcatatatcacgaggagat-------------------------------
|| || ||||  || || ||||| || || || ||||||||||| || ||||| ||||| ||||| || |||||||| ||||||||||||||||| ||||||  | |  |    | |   | | |  ||        |   ||  |   ||| | ||  ||    |     ||| ||||| ||| ||||  ||| |  |                               
GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACTCGCCGTGGCCAAGTTCTGGAAGTTGACGGTGAAAAGGCTGTTGTGCAGgttatcatttttctatttttatgaatatcttttttgcttgagattgt--attcagatt--tgcatttaccctatgatagttccat-tatccagagcacttacgttttattactgacttacttgattttcag

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 4
GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctactgacttctccctaactgcctaacgcatctctaatcatctgttctgcttcttgagactgggagatggtagttgcatatatcacgaggagat------------------------------
|| || ||||  ||||| ||||| || || ||  | |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||||| ||||||      |      ||   |  ||       | |  || ||  ||   |  || || |  ||  |||     | |||  |  ||| ||  ||  |  |                              
GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAGgttacttctccattgccttattgtcttttagtagtagttccaa--attgatgttgattttacagtatggttag-gctag--gtctatttcctgaaaacttagtttgttaattaactgcattattcatcag

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G094497_T02 (Zea mays), 5'ss of exon 3
GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctactgacttctccctaactgcctaac-gcatctctaatcatctgttctgcttcttgagactgggagatggtagttgcatatatcacgaggagat-------------------------------
               || ||||| || || ||  | |||||||| || | ||| ||||| ||||| || ||||||||||| ||||| |||||||| ||||||      |     ||    |   |   || | | |  ||||||  |   || || ||||  ||  |||   ||| ||||| |||   || |    |  |                               
---------------GAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAGgttacttctccattctcctgattgttttttagcagtagttctaat--ttgattttgattctgcagtatggtc-atgttagttccat---tcccagaaaacttagtttgttaattaactgcattattcatcag

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 4
GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctactgacttctccctaactgcctaac-gcatctctaatcatctgttctgcttcttgagactgggagatggtagttgcatatatcacgaggagat-------------------------------
|| || ||||  ||||| ||||| || || ||  | |||||||| || | ||| ||||| ||||| || ||||||||||| ||||| |||||||| ||||||      |     ||    |   |   || | | |  ||||||  |   || || ||||  ||  |||   ||| ||||| |||   || |    |  |                               
GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAGgttacttctccattctcctgattgttttttagcagtagttctaat--ttgattttgattctgcagtatggtc-atgttagttccat---tcccagaaaacttagtttgttaattaactgcattattcatcag

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 4
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 5
GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctactga-cttctccctaactgcctaacgcatctctaatcatctgttctgcttcttgagactgggagatggtagttgcatata-tcacgaggagat--------------------------------------------------
|| ||||| |  ||||| ||||| ||||| ||  | || ||||||||||| || ||||| ||||| || ||||||||||| || || ||||||||||||||||    | |   | ||||       |  |   ||  ||||  || ||   | || | ||| |      |   | |||  |  || || ||  |   ||                                                    
GGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAGgtttcttgaatcttcctctcttctttagttttctgctcctcttgtc-tccactttgatgcttaattgaacgcatttgtaaatcaatgtaatcttgcatagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccag

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 4
GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgt--ttgcctactgac-ttctccctaactgcctaacgcatctctaatcatctgttctgcttcttgagactgggagatggtagttg-catatatcacgaggagat
||||| || | |||||||||||| |||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||||||||| || || ||||| |||||  || |    ||   |||||| | |    || |    | |  | |      || | | |  | | |  |    ||  |  |   ||  ||||||        
GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactgtttggtattctccattatgtgctcatttttttgaagttcatgattatacattcttaaatggtttcatatttttaaacacctatcacattt----

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|209723248|gb|BW675195.1|BW675195
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|298183011|gb|HO028274.1|HO028274
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|213617416|gb|DB965231.1|DB965231
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|6567285|gb|AW234896.1|AW234896
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|5342420|gb|AI794704.1|AI794704
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|213607123|gb|DB967000.1|DB967000
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|10709431|gb|BF009155.1|BF009155
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|7589581|gb|AW705352.1|AW705352
EST:     GTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: GTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|213592755|gb|DB957813.1|DB957813
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
EST: gi|213602215|gb|DB958475.1|DB958475
EST:     CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG                         GTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctac ... cattcaccagGTCTTTGAGGGTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGgtttgcctactgacttctccctaactgcctaacgcatctctaatcatctgttctgcttcttgagactgggagatggtagttgcatatatcacgaggagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT