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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acccaagtactaatagtattttaacctaggttagttatcccccgtggtagaagcagttaaggaaaaataactgtacttagtacttacctttttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAAATTATAGTCTTCGAAAGGGGCAACCTCATCTTTGTCTTCAATTTTCATT

Basic information

species Glycine max
transcript GLYMA19G37750.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37750.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 19
acccaagtactaatagtattttaacctaggttagttat-cccccgtggtagaa-gcagttaaggaaa-aataactgtact--tagtacttacctttttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAAATTATAGTCTTCGAAAGGGGCAACCTCATCTTTGTCTTCAATTTTCATT
   ||| |  ||   ||||||| |      ||| |  | | |  | |  || | ||  | | || ||  | || | | ||  |   | || |  | |   |||||||||||||  |||| |||||||||||||| |||||| |||| |  || ||  | || || ||||||| |||  |  |  | ||||| ||||| || || |
---caactcttag--gtattttcatgatcattaatagtactctggagacagcacgccataatggtaacgaaaaattttctgatgaaatttgctgtgtaattgcagTTCATGACATCTGATCACCAGTATATTTCCCGGAAACATGAGGAGGATAAGGTGATTGTGTTCGAAAAGGGAGATTTGGTATTTGTGTTCAACTTCCACT
















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|26057268|gb|CA800182.1|CA800182
EST:     GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
genomic: GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
EST: gi|209702274|gb|BW677969.1|BW677969
EST:     GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
genomic: GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
EST: gi|7283403|gb|AW596011.1|AW596011
EST:     GGATGCAAGAATCTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAATGTGACAAA
genomic: GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
EST: gi|22523453|gb|BU082264.1|BU082264
EST:     CTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
genomic: CTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
EST: gi|20498242|gb|BQ273172.1|BQ273172
EST:     GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACCAGTATATTTCACGGAAGAATGAAGGTGACA
genomic: GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACA
EST: gi|6916123|gb|AW397653.1|AW397653
EST:     GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACGCAGTATATTTCACGGAAAAATGAAGGTGACAA
genomic: GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCAC-CAGTATATTTCACGGAAAAATGAAGGTGACAA
EST: gi|19347171|gb|BM892051.1|BM892051
EST:     GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
genomic: GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
EST: gi|15285214|gb|BI469105.1|BI469105
EST:     GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
genomic: GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
EST: gi|207706010|gb|GD687842.1|GD687842
EST:     GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACTGCTGAGCACCAGTATATTTCAC
genomic: GGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCAC
EST: gi|298176060|gb|HO015465.1|HO015465
EST:     AGGCTATGCAGCACCTAGAAGAAAAGTTTGGT                         TTCATGACCGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA
genomic: AGGCTATGCAGCACCTAGAAGAAAAGTTTGGTgtaagtcttc ... tttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtagaagcagttaaggaaaaataactgtacttagtacttacctttttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAAATTATAGTCTTCGAAAGGGGCAACCTCATCTTTGTCTTCAATTTTCATT
                                   tacttac  putative branch site (score: 1)
                                     cttacctttttgct  CT-rich tract
           ttaaggaaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acccaagtactaatagtattttaacctaggttagttatcccccgtggtagaagcagttaaggaaaaataactgtacttagtacttacctttttgctgcagTTCATGACTGCTGAGCACCAGTATATTTCACGGAAAAATGAAGGTGACAAAATTATAGTCTTCGAAAGGGGCAACCTCATCTTTGTCTTCAATTTTCATT

- -caagtac
- - - - - - - - - - - - - - - - - - atccccc
- - - - - - - - - - - - - - - - - - - - - -gtggtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtact