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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaattactaaacaatattgcaaaacttttttttgtctttccctcttctaaacaatattgtaaaactttttttttttgtttgtttgcctttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCATTAGAACCAGGAAGGGTAACATTTGAAGACAAAATGGCTGTAAGGAAAG

Basic information

species Glycine max
transcript GLYMA16G17680.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17680.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 1
-----actaattactaaacaatattgcaaaacttttttttgtctttccctcttctaaacaatattgtaaaactttttttttttgtttgtttgcctttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCATTAGAACCAGGAAGGGTAACATTTGAAGACAAAATGGCTGTAAGGAAAG
     | ||||| |   ||  | |||     | |     ||| |||      || | |  | | | ||| | |  |  |  |||| |       |||    | |||| ||||||||||| || |||||  | |||||||||||||||||  ||||| | ||||||||||| ||||||||||| || || |||  ||| ||||  |
ctcctagtaatttcctcacccttttgatgggcctgcc--tgtatttattctatcaacatcaaaatctaagattgataataattgtgtacaaaattttg---gcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG

upper sequence: GLYMA16G17680.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0053g00460.t01 (Vitis vinifera), 3'ss of exon 1
-----actaattactaaacaatattgcaaaacttttttttgtctttccctcttctaaacaatattgtaaaactttttttttttgtttgtttgcctttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCATTAGAACCAGGAAGGGTAACATTTGAAGACAAAATGGCTGTAAGGAAAG
     | ||||| |   ||  | |||     | |   | | | | | | | |    | ||| | | ||| | |  |  |  |||  |||     |||    | |||| ||||||||||| || |||||  | |||||||||||||||||  ||||| | ||||||||||| ||||||||||| || || |||  ||| ||||| |
ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattc-tatcaacatcaaaaatctaagattgataataattg--tgtcaaaattttg--gcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAAGG
















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|192314100|gb|FK011472.1|FK011472
EST:     CTCTGCAACTCAAACTCGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|298192406|gb|HO036488.1|HO036488
EST:     CTCTGCAACTCAGACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|298173082|gb|HO020066.1|HO020066
EST:     CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGGATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|18717665|gb|BM522981.1|BM522981
EST:     CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|209703309|gb|BW653240.1|BW653240
EST:     CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|209709206|gb|BW657175.1|BW657175
EST:     CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|13478703|gb|BG508072.1|BG508072
EST:     CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|298195348|gb|HO039179.1|HO039179
EST:     CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|37994335|gb|CF806081.1|CF806081
EST:     CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
EST: gi|16104784|gb|BI892524.1|BI892524
EST:     CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAG                         CGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA
genomic: CTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttg ... ttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctaaacaatattgtaaaactttttttttttgtttgtttgcctttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCATTAGAACCAGGAAGGGTAACATTTGAAGACAAAATGGCTGTAAGGAAAG
 ttctaaa  putative branch site (score: 2)
                     ctttttttttttgttt  putative PPT
     aaacaatattgtaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaattactaaacaatattgcaaaacttttttttgtctttccctcttctaaacaatattgtaaaactttttttttttgtttgtttgcctttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCATTAGAACCAGGAAGGGTAACATTTGAAGACAAAATGGCTGTAAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA