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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCAGAAAATATTTATTGAATACATAATGCTTGATGGGGTGAACGACGAAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactcaactgcttcttcctttctctattcaatattcaatgtctctaccaaacatttatgctctgcccccataattccaatgccactcttctactc...

Basic information

species Glycine max
transcript GLYMA11G00390.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G00390.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv03s0091g00820.t01 (Vitis vinifera), 5'ss of exon 6
TCTGCAGAAAATATTTATTGAATACATAATGCTTGATGGGGTGAACGACGAAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactcaactgcttcttcctttctctattcaatattcaatgtctctaccaaacatttatgctctgcccccataattc-caatgc-cactcttctactc-
|   |||||||| |||||||| |||||||||||||||| |||||| || |||||||| ||||| ||||   | || ||| || |||||||||||||||||||||   ||  | | |   || ||   |  |    | | ||    ||   |         ||||    |    |||| ||  ||||        | ||  |  
TGGACAGAAAATCTTTATTGAGTACATAATGCTTGATGAGGTGAATGATGAAGAGCAACATGCTCACCAGCTTGGGAAATTGCTGGAGACATTTCAAGTGgtaagatctatatttcaaattactgcatgca---gaaactctgcttcatcatgcttttgctatgaagagtgtgcatatttttcaatatgtggattactgatta
















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|193348593|gb|FK314407.1|FK314407
EST:     AGAGCACCATGCCCACCTATTGGGAAAAACTGTTGGAGACATTTCAAGTG                         GTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
genomic: AGAGCACCATGCCCACCTATTGGG-AAAACTGTTGGAGACATTTCAAGTGgtaaatactc ... tttgaaacagGTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
EST: gi|21889710|gb|BQ742923.1|BQ742923
EST:     AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTG                         GTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
genomic: AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactc ... tttgaaacagGTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
EST: gi|209719706|gb|BW672108.1|BW672108
EST:     ATTGGGAAAACTGTTGGAGACATTTCAAGTG                         GTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
genomic: ATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactc ... tttgaaacagGTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
EST: gi|207766696|gb|GD738324.1|GD738324
EST:     AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTG                         GTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
genomic: AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactc ... tttgaaacagGTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
EST: gi|12688313|gb|BG154649.1|BG154649
EST:     AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTG                         GTTGTGAACTTAATACCTTTCAACCTCTTAT-GGTACCTTGAGTCAATTCA
genomic: AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactc ... tttgaaacagGTTGTGAACTTAATACCTTTCAAC-TCT-ATTGGTACCTTGAGTCAATTCA
EST: gi|208306929|gb|GE102407.1|GE102407
EST:     AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTG                         GTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
genomic: AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactc ... tttgaaacagGTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
EST: gi|151412843|gb|EV282655.1|EV282655
EST:     AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTG                         GTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
genomic: AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactc ... tttgaaacagGTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
EST: gi|22928500|gb|BU545639.1|BU545639
EST:     AAGAGCACCATGCCCACCTATTGGGAAAACTGNTGGAGACATTTCAAGTG                         GTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA
genomic: AAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactc ... tttgaaacagGTTGTGAACTTAATACCTTTCAACTCTATTGGTACCTTGAGTCAATTCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCAGAAAATATTTATTGAATACATAATGCTTGATGGGGTGAACGACGAAGAGCACCATGCCCACCTATTGGGAAAACTGTTGGAGACATTTCAAGTGgtaaatactcaactgcttcttcctttctctattcaatattcaatgtctctaccaaacatttatgctctgcccccataattccaatgccactcttctactc

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcccc