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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatcgctactactcactatttctcgtgtttttcccaaattagccctcgttcgtagctactagtacaagctcgtttggttcggttttggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCACGGGAAATCCACGTTGGCGGATAAGTTGCTTCAGGTTACCGGCACGGTGC

Basic information

species Glycine max
transcript GLYMA04G38360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------------gtatcatcgctactactcactatttctcgtgtttttcccaaattagcc-ctcgttcgtagctactagtac-aagctcgtttggttcg-gttttggttttc-agGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCACGGGAAATCCACGTTGGCGGATAAGTTGCTTCAGGTTACCGGCACGGTGC
                                                                      ||  |         | |||   |      ||   |||| | ||| |   |  || ||| |||  |   |   | |||| || ||  | ||| || | | | |||| || ||    || || ||||||||| |||| ||||||||||| ||||| |||||||| ||| ||||||||||  ||||| || | || || |||||||
gtagtcgccccatcgcgcgcctcgcttgttagtatcacttaggtctaggcgcgcctttgggcttgctcgagtgacgaacacgaaattcagggtagagtttgcgattccgatattcgtttcaagtgcgttgctgttgtgattgatctcgattcgtcggtgttctgctctactagGTTCCCGTTTCGAACATCAGGAACTTCAGCATTATTGCGCATATCGACCATGGGAAATCGACGCTGGCGGATAAACTGCTTGAGCTCACGGGGACGGTGC

upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------gtatcatcgctactactcactatttctcgtgtt--tttcccaaattagccctcgttcgtagctactagtacaagctcgtttggttcggttttggtttt--cagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCACGGGAAATCCACGTTGGCGGATAAGTTGCTTCAGGTTACCGGCACGGTGC
                                                     |||| ||   || |  |   | | |    || |  |||||   |||       |   ||    | |||     | |  || ||  ||  ||| ||  |   |||||||  |    ||||| ||||||||||||||||| ||||| |||||||| || || |||||  ||||||||||| ||||  || |||| ||||||||||
gtagccgcctgcccgtcgttactcgttagcgaggcagcgatttatttcatgttgtattatttataatcgtgtatgtatacattggtgatttccactattgcgttgtgccggtgctcattagcgt--gttatttcggcgcgtgttttgtcctgctagGTGCCCATTTCGAATATCAGGAACTTCTGCATCATCGCGCACATTGACCATGGCAAGTCCACACTGGCGGATAAGCTGCTGGAGCTTACTGGCACGGTGC

upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 1
---gtatcatcgctactactcactatttctcgtgtttttcccaaattagccctcgttcgtagctactagtacaagctcgtttggttcggttttggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCACGGGAAATCCACGTTGGCGGATAAGTTGCTTCAGGTTACCGGCACGGTGC
   |  |  |   |  | ||| || ||  ||  || |  |  || ||        || | |  |  |  |  || ||   || |||  |      ||  ||||| ||  |    || || ||||| ||  | || || || |||||||| || |||||||| ||||| |||||||||||||||||||| || || || || |
gtcgggttctgttttgttctctctcttcatc-cgtgtgccgaaacttgagaagaatttggatttttt--ttgaaactgaatttgttatg---aaattcgcagGTTCCAATTTCGAACATCAGGAATTTTAGTATTATAGCTCATATTGATCATGGGAAATCTACGTTAGCGGATAAGTTGCTTCAGGTGACTGGTACTGTTC

upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 1
-gtatcatcgctactact--cactatttctcgtgtttttcccaaattagccctcgtt-cgtagctactagtacaagctcgtttggttcggttttggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCACGGGAAATCCACGTTGGCGGATAAGTTGCTTCAGGTTACCGGCACGGTGC
 | |   |      ||||  ||  |||  |  || | ||      ||     | |    |    |  || |  | |||  ||| |||    |||    | ||||| ||  |    ||||| ||||| |||||||| ||||| |||||||| || |||||||| || || || ||||||||||| ||  | || || ||||| |
gggactttacactttactggcaaaattattgatggtgttaaggttttgttttttgacatgggaatcttactgaatgctatttttgtt---gtttaaaatgcagGTTCCAATATCAAATATCAGGAATTTCTGCATAATTGCTCATATTGATCATGGGAAATCAACTTTAGCAGATAAGTTGCTGCAAATGACGGGTACGGTAC

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|16284870|gb|BI946314.1|BI946314
EST:     GCACCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCGTCTCTCTAAG                         GTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
genomic: GCATCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCGTCTCTCTAAGgtatcatcgc ... tggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
EST: gi|213590480|gb|DB968072.1|DB968072
EST:     GCACCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCGTCTCTCTAAG                         GTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
genomic: GCATCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCGTCTCTCTAAGgtatcatcgc ... tggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
EST: gi|20207740|gb|BQ133829.1|BQ133829
EST:     GCACCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCGTCTCTCTAAG                         GTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
genomic: GCATCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCGTCTCTCTAAGgtatcatcgc ... tggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
EST: gi|16284257|gb|BI945987.1|BI945987
EST:     GCACCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCGTCTCTCCAAG                         GTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
genomic: GCATCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCGTCTCTCTAAGgtatcatcgc ... tggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
EST: gi|213602994|gb|DB958582.1|DB958582
EST:     CACCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATCAG-CTCTCTAAG                         GTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC
genomic: CATCGACTTCGAATCCGCCGCCAAAGCCGGAGAGGATC-GTCTCTCTAAGgtatcatcgc ... tggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccctcgttcgtagctactagtacaagctcgtttggttcggttttggttttcagGTGCCGGTGCGTAATATAAGGAACTTCTGCATCATTGCGCATATTGACCACGGGAAATCCACGTTGGCGGATAAGTTGCTTCAGGTTACCGGCACGGTGC
                                                ttttc  CT-rich tract