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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgttacattctgctaacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT

Basic information

species Glycine max
transcript GLYMA09G13840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgttacattctgct--aacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT
              ||| || |  |   |||   ||  | ||   | |  |  ||   |   | ||| ||||   ||  ||||   |  || || |||  |   | ||  | |||               |||| ||||||||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||||| 
-------------tcttcttgtccttgttggtccaa--actgccag-tacttaaacacgcactgcatcctgcatgaatgttttcttatgag-ataacttgatttcattattttgt---------------agGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g73300.1 (Oryza sativa), 3'ss of exon 3
gcatataaatacccctttttatgttgtctggcaaaacaattgtttgatt--ttctaaattgtgttacattctgctaacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT
                             ||| | |  ||| | |  ||  || | ||  |||   |  |   || |  |  ||  |    ||    || ||   |||  |       | | |  ||| ||||||||||||||||| ||||||||| ||||||| ||||| || ||||||||||| || || || |||
-----------------------------ggccatattattttcttgttaattgtcaacggtgcaccgcttaactga--tgcttgtattgttaaacatctaatttcttgcttcccaattattat-tctgcagGATCCTGCAGAGGCTGACAAGTTGCTGAAAATTCAGAGGGATTTGGATGAAACTAAGATTATTCTT

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 4
gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgttacattctgctaacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT
                      ||| | |||   |  | | | ||   |  ||  |||   ||||| |||     |||  | | | ||| || | ||| ||  ||     | |     |||    |  |||||||||| || || ||||| || |||||||| ||||| || ||||||||||| ||||| ||||| 
----------------------gttatgtggttga-tattggatta--tgcctgtattcctttacactctatctgcctcataa-agaagcat-attcacactactcatgatatgttcatca---ttgtagGATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 3
gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgtt--acattctgctaacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT
                      ||| |      |   | || ||||  | | | |||  ||||  | | | |   ||| | ||| |       ||  ||||      |||  | ||  ||  | |||||||||| || ||||| || || ||| || ||||||||||||| || |||||||| ||||| || ||||||
----------------------gttctagaagcactaacttttttgtatctatgaatcttgtttaagactttaggaac-tatttgc-------tgtgtcaattattcttacttttttttggaatatcttcagGACCCGGCAGAAGCTGATAAGCTGTTGAAAATCCAGAGGGAATTGGATGAGACCAAGATTATCCTT

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgttacattctgctaacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT
                 || || ||    | |    | ||||||| ||       |   ||||  ||| ||  |    ||| |    |   ||| |        ||   | ||   |||  ||||||||||| || |||||||| || ||| || ||||||||||||| ||||||||||| || || || ||||||
---------------aattaattttagtagccc---ccattgttttat------gaccatgttggattttg--agtgatttgatcttaaattgattttggga--ttgtcccgtatttgt--aatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------gcatataaatacccctt-tttatgttgtctggcaaaacaatt--gtttgattttctaaattgtgttacattctgctaacctttttacacaagtatgactcaaacccctttat---ctgttc-ctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT
                                              |||||||  |||   |  ||| | |||  |   |||  | ||   ||| ||||  |   || |  |  ||  | | | |   | |   ||  ||| || ||||   |||| |   |||||| || | |||||||||||||||||| ||||| || |||||| ||||||| |||||||||||||||||||| ||||| || |||
gtatttctccacatttttctcattttgtttgttgcgtcataaggctgcatataggtacaattaattttttttgcatcataaactatttcaattttatttgttcctttcttcttaatggttcaagc---tatggtcatttataacccaaaatactttttattctgttctctttgaaatcttcagGATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT

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|298197641|gb|HO045120.1|HO045120
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
EST: gi|192313879|gb|FK011083.1|FK011083
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
EST: gi|192321645|gb|FK013989.1|FK013989
EST:     TCTGGCAAAATTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
genomic: TCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
EST: gi|298168934|gb|HO009864.1|HO009864
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAACTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
EST: gi|298164125|gb|HO013770.1|HO013770
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
EST: gi|298163467|gb|HO012200.1|HO012200
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
EST: gi|192333542|gb|FK025737.1|FK025737
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
EST: gi|31469010|gb|CD411038.1|CD411038
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAA
EST: gi|298172019|gb|HO021611.1|HO021611
EST:     ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAG                         GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATG
genomic: ACAGTACTCAACCATGGCCCTATTTGAATGAAGCTCTGGCAAAATTCCAGgcatataaat ... aaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT
                                                tcttc  CT-rich tract
                             tttatct  TA-rich tract