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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTGCTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttggtttggtcaagccttgtacaaactcaagtttcatcttataattgctgctaagtataattctgttactatgcttatagtttggtagaatttt...

Basic information

species Glycine max
transcript GLYMA18G35450.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G35450.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G26840.1 (Arabidopsis thaliana), 5'ss of exon 2
ACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTGCTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgta-aatttggtttggtcaagccttgtacaaactcaagtttc--atcttataattgctgctaagtataattct-gttactatgcttatagtttggtagaatttt
 |||||||| || |||||||| || |||||||| ||  | ||||| ||||||||||||||||||||  |  | || || || || || || || ||||||||| ||  |   ||   || || || |     || |  |||   |  ||||| || ||| ||   |||||||| |  ||||                       
GCTGATGAATGCTTACTGTGACCGGCAATCTGTGGACATGAACTCCATTGCTTTCTTGTTTGATGGGCGTCGTCTTCGTGCTGAGCAAACTCCCGATGAGgtataacattcattctacatgctttattt---cttaccttttgaagtttatagtttctgatactaataattcttgacactacag--------------------

upper sequence: GLYMA18G35450.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
ACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTGCTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttggtttggtcaagccttgtacaaactcaagtttcatcttataattgctgctaagtataattctgttactatgcttatagtttggtagaatttt
||||||||| || |||||||| ||||| ||||| ||||| ||||||||||||||||||||||||||  |  | || || || || ||||| || ||||||||||  |   | |    |  || |   |     |   ||||   || | |  | ||     | |  ||     |  ||  |   | |||   ||      
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttc--aattttacag------

upper sequence: GLYMA18G35450.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv12s0059g01310.t01 (Vitis vinifera), 5'ss of exon 2
ACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTGCTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttggtttggtcaagccttgtaca-aactcaagtttcatcttataattgctgctaagtataattctgttactatgcttatagtttggtagaatttt
 || ||||| || || ||||| || |||||||||||  | ||||| ||||| ||||||||||||||  |  | ||||| | |||||| |||||||||||||||  | |   |   |  |  ||| | |   | |     | ||       |||||    | |  | || || |||   | | | | | ||   ||      
GCTCATGAATGCTTATTGTGACCGACAATCTGTAGACCTCAACTCGATTGCATTCTTGTTTGATGGTCGTCGTCTCCGGGGAGAACAAACCCCTGATGAGgta--tctctctcattttaatcttatccttgagttggaatccaatgccccattgcctggatgcctgatgcttttatctttccttt-gcttcacag------

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|151408251|gb|EV278059.1|EV278059
EST:     TTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: TTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|213604768|gb|DB956109.1|DB956109
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|151395673|gb|EV265550.1|EV265550
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATAGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|193343853|gb|FK310325.1|FK310325
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGG
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGG
EST: gi|151399595|gb|EV269466.1|EV269466
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|193539458|gb|FK494746.1|FK494746
EST:     CAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|192310968|gb|FG998916.1|FG998916
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|24136264|gb|BU926774.1|BU926774
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|213612132|gb|DB974552.1|DB974552
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|151407669|gb|EV277484.1|EV277484
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATACTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|192310967|gb|FG998915.1|FG998915
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|192308691|gb|FK000081.1|FK000081
EST:     TTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCTCC-GATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTACACCAAACCGG
genomic: TTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACC-CCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGG
EST: gi|192319169|gb|FK009109.1|FK009109
EST:     CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
EST: gi|193678513|gb|FK617993.1|FK617993
EST:     CAGACCCCTGATGAG                         CTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA
genomic: CAGACCCCTGATGAGgtaaatttgg ... ttttgtgcagCTAGAGATGGAGGATGGTGATGAGATAGATGCAATGCTGCACCAAACCGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTGCTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttggtttggtcaagccttgtacaaactcaagtttcatcttataattgctgctaagtataattctgttactatgcttatagtttggtagaatttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG