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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctaaacatatttcttgaattatgtatacataaattcctgagctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG

Basic information

species Glycine max
transcript GLYMA20G37330.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g29540.1 (Oryza sativa), 3'ss of exon 9
tttttctaaacatatttcttgaattatgtatacataaattcctgagctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG
                          | | ||  |   |||  || | |     |  || || |     ||||| ||| |       | |   | ||||||| |||||||||||  | ||||| |||||||||   ||||||||||||||||| || ||||| || || 
-------------------------gtatctatctgctttcgagaaccaaagcctgaaagcttgtt---gttagctaacaa------attacatttacagGTCTGTGATTTTGGACTTTCACGTTTGAAGCACGGTACATTTTTGTCATCCAAATCCACTGCAGGGACT

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 9
tttttctaaacatatttcttgaattatgtatacataaattcctgagctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG
   | ||   |   | | || |  | |  || |||  | || | || |||||   |   |   |    | |   | |  | | |        |   | |||| |||||||||||  | ||||| ||||||||||  ||||| || |||||||| || ||||||||||| 
--gtactgtgc---tctttttacctttacattcattcagtcataag-tatttatgagcgtgctgatcgattggctcaccaatga------tgtgaaatagGTTTGTGATTTTGGACTTTCACGCTTGAAGCACAGTACATTCTTATCATCCAAATCCACTGCTGGAACT

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G175563_T01 (Zea mays), 3'ss of exon 9
tttttctaaacatatttcttgaattatgtatacataaattcctgagctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG
                          ||| |         |  ||   || ||     | | |   | | | |  | ||  || || |    |   |||||| ||||| |||||  | || |||||||||||||  ||||||||||||||||| || || |||||||| 
-------------------------gtgtgtgatcttgcccacgattaatatttggccaccaataatcattcacatcaatatatgcaa----tataacagGTTTGTGACTTTGGACTTTCGCGGTTGAAGCACAGTACATTTTTGTCATCCAAATCTACAGCTGGAACA

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 9
tttttctaaacatatttcttgaattatgtatacataaattcctgagctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG
  |    | || | |||||| | || |  | ||  | || | ||     | | ||   |  ||     | || |||     ||    |||     |  ||||  |||||||||||||||| || || |||||||| || ||||| || ||||| |||||||||||||||
-gtaggaagacttttttcttaagttgtcca-acgaatatacttgtttactctaatggtaaataaatagattttgtttt---tatcttactaaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 9
tttttctaaacat--atttcttgaattatgtatacataa-attcctgagctatttta-tataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG
     | ||  ||  |   |   ||      | | |||| ||||     |  || |  | | |  ||   ||  ||  |  |   |||   |    || | ||||||||||||||||||||||||||  |||||||||||||||||||||||||||| |||||||||||||||
---acccaagtattaagaacggaaaaacaacaaaaataatattctatcacagttgtggtttgacatacaatatcttcatggaccataatttatgactt-tgcagGTATGTGATTTTGGGTTGTCACGCCTGAAGCACAACACATTTTTGTCATCCAAATCAACTGCTGGAACG

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|51338473|gb|CO982339.1|CO982339
EST:     GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG                         GTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
genomic: GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAGgtatatgatt ... ctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
EST: gi|298181852|gb|HO026027.1|HO026027
EST:     GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG                         GTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACTTTTTTGTCATCC
genomic: GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAGgtatatgatt ... ctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
EST: gi|4396654|gb|AI495651.1|AI495651
EST:     GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG                         GTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
genomic: GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAGgtatatgatt ... ctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
EST: gi|19054297|gb|BM732964.1|BM732964
EST:     GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG                         GTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
genomic: GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAGgtatatgatt ... ctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
EST: gi|33389731|gb|CA852938.1|CA852938
EST:     GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG                         GTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
genomic: GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAGgtatatgatt ... ctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
EST: gi|151393400|gb|EV263275.1|EV263275
EST:     GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG                         GTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC
genomic: GAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAGgtatatgatt ... ctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG
                                        ccactctttct  CT-rich tract
     tttatataatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctaaacatatttcttgaattatgtatacataaattcctgagctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - -ctaaaca
- - - - - - - - - - - - - - - - - - -attcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agccact