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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTGGTCCCTATCCTGCTGCTCAGGTTGTGAGAGATTTCCAAGGCAAATTTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatcctctattaatctcttttcattttcatgtcatatttgctaatggttctcttctctaacgtggcatatatctcctggtcttttacag

Basic information

species Glycine max
transcript GLYMA20G28930.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28930.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0020g04160.t01 (Vitis vinifera), 5'ss of exon 2
TCGTGGTCCCTATCCTGCTGCTCAGGTTGTGAGAGATTTCCAAGGCAAATTTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatcctct-----attaatct--cttttcattttca--tgtcatatttgcta-------------atggttctcttctct-aacgtggcatatatctcctggtcttttacag-------------
| | ||||| |||||||| | ||| |||||||||||| |||| || |||||||||||| |||| ||||||||   |   |  || |||||| | ||||| |||||| | ||| |     | |||| |  || | || |||||  | ||    ||| |              ||| |   ||||| | || |  || || |||   ||    |||||               
TAGAGGTCCATATCCTGCAGATCAAGTTGTGAGAGATCTCCATGGGAAATTTGCATTTGTTCTCTATGACAGCTCTAACAGAACTGCATTTCTAGCTGCTgtgagtaaaccttttggccagtaattttgctatccaatttcaagtatccctcttgttgctctcagattgttatgatcaccttctttgaaggcagcttacatcaggtgtaactttacccacatgtaatgcag

upper sequence: GLYMA20G28930.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0036g00050.t01 (Vitis vinifera), 5'ss of exon 3
TCGTGGTCCCTATCCTGCTGCTCAGGTTGTGAGAGATTTCCAAGGCAAATTTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatcct-----ctattaatct--cttttcattttca--tgtcatatttgcta-------------atggttctcttctct-aacgtggcatatatctcctggtcttttacag-------------
| | ||||| |||||||| | ||| |||||||||||| |||| || |||||||||||| |||| ||||||||   |   |  || |||||| | ||||| |||||| | |||     ||| |||| |  || | || |||||  | ||    ||| |              ||| |   ||||| | || |  || || |||   ||    |||||               
TAGAGGTCCATATCCTGCAGATCAAGTTGTGAGAGATCTCCATGGGAAATTTGCATTTGTTCTCTATGACAGCTCTAACAGAACTGCATTTCTAGCTGCTgtgagtaaaccttttggctagtaattttgctatccaatttcaagtatccctcttgttgctctcagattgttatgatcaccttctttgaaggcagcttacatcaggtgtaactttacccacatgtaatgcag
















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|209702369|gb|BW656344.1|BW656344
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|6727143|gb|AW311497.1|AW311497
EST:     AGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: AGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|15662969|gb|BI700340.1|BI700340
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|151404166|gb|EV273976.1|EV273976
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|21888440|gb|BQ741653.1|BQ741653
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|23728218|gb|BU762155.1|BU762155
EST:     GACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: GACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|19934623|gb|BQ079653.1|BQ079653
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAA
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCT-GATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAA
EST: gi|10845849|gb|BF068885.1|BF068885
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|209702370|gb|BW656345.1|BW656345
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|22523132|gb|BU081943.1|BU081943
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|151401746|gb|EV271559.1|EV271559
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|120494313|gb|EH222480.1|EH222480
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGCGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|19935707|gb|BQ080551.1|BQ080551
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|209700713|gb|BW670475.1|BW670475
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|151409949|gb|EV279757.1|EV279757
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|15813151|gb|BI785426.1|BI785426
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|21595604|gb|BQ610543.1|BQ610543
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|192307091|gb|FK000041.1|FK000041
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatc ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTGGTCCCTATCCTGCTGCTCAGGTTGTGAGAGATTTCCAAGGCAAATTTGCATTTATTCTGTATGACAGTGGTTCTAAGACCGCATTTGTTGCTGCGgtgagttatcctctattaatctcttttcattttcatgtcatatttgctaatggttctcttctctaacgtggcatatatctcctggtcttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC