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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaataaatgagtgtagatatagattgattaatgtttatgtagtattcaacaattatgggggtctttagacattgataattctcattgcgttgtttatattgcatgtgaaaaaagatctaacaaatgcttctaactagcttgtttctatgatcacatatgtggttttgttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGCCAAGAATGCAAGACCATTGTTGCAGAGTATGGACAAACAATATTGGATT

Basic information

species Glycine max
transcript GLYMA17G01500.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01500.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G11910.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgaataaatgagtgtagatatagattgattaatgtttatgtagtattcaacaattatgggggtctttagacattgataattctcattgcgttgtttatattgcatgtgaaaaaagatctaacaaatgcttctaactagcttgtttctatgatcacatatgtggttttgttct-tgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGCCAAGAATGCAAGACCATTGTTGCAGAGTATGGACAAACAATATTGGATT
                                                                                     | |    |   || | ||||| | |  |     ||  ||  |  | || |   || || || | | |  | | || |    ||||   || |||||||| | || || |||||||||||||| ||||||||| |||||||| | |||||  | ||||||||  |||| |   | || || || || || |||||||
------------------------------------------------------------------------------------gtaagcaaga-attaaaattgcttat--agctttatagaattatggttttt---taactagtatatgtagtaatatttcaattttttccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTGGATCAATACGGGCAGACCATTTTGGATT

upper sequence: GLYMA17G01500.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G62290.2 (Arabidopsis thaliana), 3'ss of exon 7
gtatgaataaatgagtgtagatatagattgattaatgtttatgtagtattcaacaattatgggggtctttagacattgataattctcattgcgttgtttatattgcatgtgaaaaaagatctaacaaatgcttctaactagcttgtttctatgatcacatatgtggttttgttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGCCAAGAATGCAAGACCATTGTTGCAGAGTATGGACAAACAATATTGGATT
                                                                           |    || |  ||       ||||||| |     |  |   || |  |  | ||| ||       |||  ||    |  |||  |   ||||  | |  || ||| ||||  |  | ||||||||  | || |||||||||||||||||| | |||||  | ||||||||  ||||||   ||||||||||||| || |||||||
--------------------------------------------------------------------------gtaagcaaataccacga----gtttatagttttatttcagttagtttgagtatatgttt-------gctc-ttgaagttctcattttcctggtaatttctttctagGCTGTGGTTGCCATGATAAATAAGGCTATTGGAGCATCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTTGACCAGTATGGACAAACCATTTTGGATT

upper sequence: GLYMA17G01500.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 8
gtatgaataaatgagtgtagatatagattgattaatgtttatgtagtattcaacaattatgggggtctttagacattgataattctcattgcgttgtttatattgcatgtgaaaaaagatctaacaa-atgcttctaactagcttgtttctatgatcacatatgtggttttgttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGCCAAGAATGCAAGACCATTGTTGCAGAGTATGGACAAACAATATTGGATT
                                                                              ||||  |    || | | |  | |   |||      |  | | || |||      |||||  |   || || | | ||     ||   || |   | |   || ||||  |  |||||||||| ||||| ||||||||  | |||||| | ||||| |||||||||||  | |||||| |||||||  |||||||  ||||||
---------------------------------------------------------------------------caaataaaacg-gctgtgatatgaa-agcccatacttttagcgctatagcaatgcatctctaaa-aatatggttgtttaattg---attcagtctgtctttctcagGCTGTTGTTGCTATGATAAATCATGCCATTGGAGCCACCGGAGTTGTTAGCCAGGAATGCAAGACTGTAGTTGCACAGTATGGGGAAACAATCATGGATT

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|193457197|gb|FK423593.1|FK423593
EST:     GCTGTTCAGCCATTGCAGACTCAGGGACTTCTTTGTTGGCAGGTCCAACG                         ACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
genomic: GCTGTTCAGCCATTGCAGACTCAGGGACTTCTTTGTTGGCAGGTCCAACGgtatgaataa ... gttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
EST: gi|193648227|gb|FK595308.1|FK595308
EST:     ACTTCTTTGTTGGCAGGTCCAACG                         ACTGTCATAGCTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
genomic: ACTTCTTTGTTGGCAGGTCCAACGgtatgaataa ... gttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
EST: gi|13790574|gb|BG653165.1|BG653165
EST:     CTGTTCAGCCATTGCAGACTCAGGGACTTCTTTGCGAAG-AGGTAAAACG                         ACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
genomic: CTGTTCAGCCATTGCAGACTCAGGGACTTCTTTG-TTGGCAGGTCCAACGgtatgaataa ... gttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
EST: gi|193680199|gb|FK625323.1|FK625323
EST:     GCTGTTCAGCCATTGCAGACTCAGGGACTTCTTTGTTGGCAGGTCCAACG                         ACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
genomic: GCTGTTCAGCCATTGCAGACTCAGGGACTTCTTTGTTGGCAGGTCCAACGgtatgaataa ... gttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
EST: gi|37996199|gb|CF807788.1|CF807788
EST:     GCTGTTCAGCCATTGCAGACTCAGGGACTTCTTTGTTGGCAGGTCCAACG                         ACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC
genomic: GCTGTTCAGCCATTGCAGACTCAGGGACTTCTTTGTTGGCAGGTCCAACGgtatgaataa ... gttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgcttctaactagcttgtttctatgatcacatatgtggttttgttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGCCAAGAATGCAAGACCATTGTTGCAGAGTATGGACAAACAATATTGGATT
      ttctaac  putative branch site (score: 1)
                                         ttttgttctt  putative PPT
                    tttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaataaatgagtgtagatatagattgattaatgtttatgtagtattcaacaattatgggggtctttagacattgataattctcattgcgttgtttatattgcatgtgaaaaaagatctaacaaatgcttctaactagcttgtttctatgatcacatatgtggttttgttcttgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGCCAAGAATGCAAGACCATTGTTGCAGAGTATGGACAAACAATATTGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA