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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaacctttttacacaattatgtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT

Basic information

species Glycine max
transcript GLYMA13G19950.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g73300.1 (Oryza sativa), 3'ss of exon 3
gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaata-ttctaaattgtgttacattctgctaacctttttacacaattatgtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT
                                                          |     |  | ||  |   || || | ||  |||   |  |   || |  |  ||  |   |||   ||    | ||   |||  |       | | |  ||| ||||||||||||||||||||||||||| ||||||||||||| || ||||||||||| || || || |||
----------------------------------------------------------ggccatattattttcttgttaattgtcaacggtgcaccgcttaactga--tgcttgtattgttaaacat----ctaatttcttgcttcccaattattat-tctgcagGATCCTGCAGAGGCTGACAAGTTGCTGAAAATTCAGAGGGATTTGGATGAAACTAAGATTATTCTT

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaacctttttacacaattatgt-atgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT
                                               |  |  |  ||||| |   ||| ||  || || |  ||   |   | ||| ||||     | ||| |    |||||  || |||  |   | ||  | |||               |||| |||||||||||||||||||| |||||||| ||||| || ||||||||||||||||| ||||| 
---------------------------------------------tcttcttgtccttgttggtccaaactgc-cagtacttaaacacgcactgcatcctgcatgaatgttttc----ttatgagataacttgatttcattattttgt---------------agGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 4
gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaacctttttacacaattatgtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT
                                                   | | | || |||| |   |||    ||   ||  |||   ||||| |||     |||     || ||  | | || | ||| ||  ||     | |     |||    |  |||||||||| || |||||||| || |||||||||||||| || ||||||||||||||||| ||||| 
---------------------------------------------------gttatgtggttgata---ttggattatgc-ctgtattcctttacactctatctgcct-----cataaagaagcat-attcacactactcatgatatgttcatca---ttgtagGATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 3
gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaacctttttacacaattatgtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT
                                                            | |   | | ||    ||   ||  ||    |||||  ||     |||  | ||  ||  ||       | |  | | |   ||      |||  | | |  |||| ||||| || ||||||||  | |||||||||||||| || ||||||||||||||||| || |||
------------------------------------------------------------tggctgatactggattatgc-ctgtatcactttacaccctatctgcctcat-acggaagcatactcacgtta--ctcatgggtcatgatatgttcattttgtagGACCCTGCGGAAGCTGACAAACTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATTCTT

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaacctttttacacaattatgtatgactcaaacccc---tttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT
                                                               ||  ||||  | | ||  |   ||||| |||    |   |    |||| |   | ||     | | |  |        ||   | ||   |||  ||||||||||| || ||||||||||| ||| || ||||||| ||||| ||||||||||| ||||| || ||||||
---------------------------------------------------------------aattaatt--ttagtagcccccattgttttatgaccatgttggattttgagtgatttgatcttaaattgattttgggattgtcccgtatttgt--aatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 3
--------------gcatgtaaatacctcttttatgttgtatgagcttcagttagagg-agttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaaccttttta---cacaattatgtatgactcaaacccctttat---ctgttc-ctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT
                 | | | |   | | ||  ||  ||   ||| ||  |||    | ||  |  ||||||  | | ||| |  |||||| ||    ||| |||| | |||| || |    || |    |   | || ||| || ||||   |||| |   |||||| || | |||||||||||||||||| |||||||| |||||| |||||||||||||||||||||||||||| ||||| || |||
gtatttctccacatttttctcattttgtttgttgcgtcata-aggctgcatataggtacaattaattttttttgcatcataaactatttcaatttt----att-tgttcctttcttcttaatggttcaagctatggtcatttataacccaaaatactttttattctgttctctttgaaatcttcagGATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT

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|298168422|gb|HO009352.1|HO009352
EST:     ACAGTACTCAACCATGGCCCAATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|192306907|gb|FK002629.1|FK002629
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|192299559|gb|FG987720.1|FG987720
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|151393215|gb|EV263090.1|EV263090
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|192306908|gb|FK002630.1|FK002630
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|151407036|gb|EV275591.1|EV275591
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|298197444|gb|HO044923.1|HO044923
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|213611777|gb|DB964781.1|DB964781
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGNAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|192294833|gb|FG987522.1|FG987522
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|298179750|gb|HO024965.1|HO024965
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|208126796|gb|GD926054.1|GD926054
EST:     ATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
EST: gi|213602294|gb|DB958554.1|DB958554
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatgtaaat ... aaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacacaattatgtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT
                                                tcttc  CT-rich tract
       aattatgtat  TA-rich tract