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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTACTCCCTACTTGGCCTCCAATAGCTCCAGTCCCCTCTGGTATGCAGTCAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatctcctctttatctacttattaatattccttacatgttgagttgaaagagaagaaattgtttttattcaatcttattcggggttacaacatg...

Basic information

species Glycine max
transcript GLYMA17G11790.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11790.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g43640.2 (Oryza sativa), 5'ss of exon 6
ACTACTCCCTACTTGGCCTCCAATAGCTCCAGTCCCCTCTGGTATGCAGTCAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatctcctctttatctacttattaatattccttacatgttgagttgaaagagaagaaattgtt---tttattcaatcttattcggggttacaacatg
   ||||| || ||||| || || |||     |||  | |||||||||||||| ||||| ||||||||||| |||||||| || |||||||| |||||||||||   |      |||| |||   |     | ||   || |||     || |    | | |||        |||| |   |       | |||    | |  
CACACTCCATATTTGGCATCAAAGAGCAGTTCTCCTATGTGGTATGCAGTCAGACGTGCATCTGCTCATATCATTGTGCTTTCTAGCTATTCTCCATTCGgtaagataaagatcctttctctgacttgctttgttttgtatatgcca--ttaagtctgtacaaaccaccagatttagt-ggtggcggctgtggtggtgatagt

upper sequence: GLYMA17G11790.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G34850.1 (Arabidopsis thaliana), 5'ss of exon 5
ACTACTCCCTACTTGGCCTCCAATAGCTCCAGTCCCCTCTGGTATGCAGTCAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaat----taat--ctcctctttatctacttattaatattccttacatgttgagttgaaagagaagaaattgtttttattcaatc-ttattcggggttacaacatg-----------------------------------------------------------
||||| || ||||| ||||| || ||   |||||| || ||||| || || |||||||| ||||||||||| ||||| || ||||||||||| || || ||||||    |||   |||  |   |||  ||  ||   | |  ||   | || | || | |   || | |||      | | | |  |||  |  |  |    | |                                                            
ACTACGCCTTACTTAGCCTCAAAAAGTAGCAGTCCTCTTTGGTACGCTGTTAGGCGTGCATCTGCTCATATCATTGTCCTCTCCAGCTATTCGCCTTTTGgtaataccttaactgctcaacaacatcccctgcttctaacttttttgttctttactttataagtaaaagatttacccaaatgagtggttaagcatgactctttcttataagtaaaagatttacccaaatgagtggttaagcatgactctttctgtgtgttgtacag

upper sequence: GLYMA17G11790.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv04s0008g06520.t01 (Vitis vinifera), 5'ss of exon 6
ACTACTCCCTACTTGGCCTCCAATAGCTCCAGTCCCCTCTGGTATGCAGTCAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatctcctctttatctacttattaatattccttacatgttgagttg-aaagagaagaaattgtttttattcaatcttattcggggttacaacatg
 |||| || ||  |||||||| | |||  || ||| || |||||||| ||||| ||||| || |||||||||||||||||||| || ||||| ||||| ||||||| |||    | || |||  || ||    |  |  |  || | |  ||  ||||  ||||||  |  ||  |   ||  | ||    ||    | ||
GCTACACCTTATATGGCCTCCCAAAGCAGCAATCCTCTTTGGTATGCTGTCAGACGTGCATCCGCTCATATAATTGTGCTATCAAGTTATTCTCCATTTGgtaattcatcattcccttctctg-ttgttgcattctcgcaggtgcttatatgtgaagattagaaatgttaatttctatgtcaaaatccattttttttcttg

upper sequence: GLYMA17G11790.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv11s0118g00240.t01 (Vitis vinifera), 5'ss of exon 6
ACTACTCCCTACTTGGCCTCCAATAGCTCCAGTCCCCTCTGGTATGCAGTCAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatctcctctttatctacttattaatattccttacatgttgagttgaaagagaagaaattgtttttattcaatct-tattcggggttacaacatg
 | || || ||    |||||||| |||   || || || ||||||||  |||| ||||| ||||||||||| ||||| || ||||||||||| ||||| |||||||  ||    |  | |||  |  ||  |         || || |  || |        |  |  | |||| | |||| ||| |      |   ||  
CCAACACCTTATGCAGCCTCCAAAAGCAGTAGCCCTCTTTGGTATGCCATCAGACGTGCATCTGCTCATATCATTGTTCTGTCCAGCTATTCTCCATTTGgtaatttttcattcccctgtctcttgtttccttcatacattatattaatctgtagctctcttatattctgttatgctatctatatgccaaacgagttcaa-

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|7692221|gb|AW760334.1|AW760334
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|208195824|gb|GD989989.1|GD989989
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAG
EST: gi|6481590|gb|AW200861.1|AW200861
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|7690913|gb|AW759049.1|AW759049
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|11273813|gb|BF324205.1|BF324205
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|7693127|gb|AW761224.1|AW761224
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|13240434|gb|BG359743.1|BG359743
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|207835765|gb|GD806504.1|GD806504
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|7796484|gb|AW781881.1|AW781881
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|7692539|gb|AW760642.1|AW760642
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|7326807|gb|AW620605.1|AW620605
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|193635387|gb|FK584782.1|FK584782
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|6481824|gb|AW201095.1|AW201095
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|6727109|gb|AW311463.1|AW311463
EST:     CACGCGTGCGTCTGCTCATATAATCGTGCTATCCAGCTATTCACCATTCG                         TGATATACACTCCTCAATACATGTAGCTTAAAGAAGAGCTGAAGCGAGTT
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTT
EST: gi|151411194|gb|EV281005.1|EV281005
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|6483125|gb|AW202317.1|AW202317
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|16996117|gb|BM085489.1|BM085489
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|207759295|gb|GD731750.1|GD731750
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|22523010|gb|BU081821.1|BU081821
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTTG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|193384819|gb|FK353177.1|FK353177
EST:     CATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|7686599|gb|AW757247.1|AW757247
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|308098822|gb|HO760663.1|HO760663
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTTG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
EST: gi|208339496|gb|GE133560.1|GE133560
EST:     CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCG                         TGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG
genomic: CAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatc ... ttcataacagTGAAATACACTCCTCAATACATGTGGCTTAAAGAAGAGCTGAAGCGAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTACTCCCTACTTGGCCTCCAATAGCTCCAGTCCCCTCTGGTATGCAGTCAGGCGTGCGTCTGCTCATATAATTGTGCTATCCAGCTATTCACCATTCGgtaattaatctcctctttatctacttattaatattccttacatgttgagttgaaagagaagaaattgtttttattcaatcttattcggggttacaacatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagaga