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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaaatgaaaattgataagcctattttagaattcagattaaatttctagattttgcactgatatttggtcatatgactattgaaatgttgcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTTAACATGAATAAT

Basic information

species Glycine max
transcript GLYMA20G35600.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------------------------------------------------------------------tttaaatgaaa-attgataagcctattttagaattcagattaaatttctagattttgcactgatatttggtcatatgactattgaaatgttgcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTTAACATGAATAAT
                                                                                   |  || ||| | | || |     |  |  ||   |  |||| |||| ||    |      | |   | | | |||| ||  |||   | ||     |  |||| ||   |||||| |||||||||||||  || |||||||||||| |||||| |||||| || 
gtactttaacattcttcatagcttttattttatcttgtagtggatggtgtgtttctttgattgctcatgtgcagctagtaaaatcaaagtgagatagtggttgctatcatcgagggctt-gatttaattgctcttctcatatttaagggtagctaatatcacctttgc--tttttgccctgtagGTGCTTGTAGAACCCAAAAATGCTCTTGGGAAACAGTACAAGAAACTATTTAGCATGAACAAC

upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 11
-----tttaaatgaaaattgataagcctattttagaattcagattaaatttctagattttgcactgatatttggtcatatgactattgaaatgttgcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTTAACATGAATAAT
     || |||  | ||||   ||   |||| |  | || | | |  ||        ||||    |    ||    |  ||  |  ||   |  |  | | |||||| ||||||||||||||||||||||||| |||||||||||||||||| |||| |||||| |||
gaaacttgaaactagaattttcaa---tattcttaattttatactgtatcctcttcatttgtgaagtagcttatgtacttgctt--tggtttcattttgtaacagGTTCTCACAGAACCAAAAAATGCTCTTGGTAAGCAGTACAAGAAATTGTTTAGCATGAACAAT
















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|193655522|gb|FK601824.1|FK601824
EST:     TTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTATGCAG                         GTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTT
genomic: TTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTATGCAGgtattatact ... gcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTT
EST: gi|22928880|gb|BU546019.1|BU546019
EST:     TTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTATGCAG                         GTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTT
genomic: TTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTATGCAGgtattatact ... gcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTT
EST: gi|16346887|gb|BI972482.1|BI972482
EST:     TTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTATGCAG                         GTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTT
genomic: TTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTATGCAGgtattatact ... gcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTT
EST: gi|17519864|gb|BM188906.1|BM188906
EST:     TTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTATGCAG                         GTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTT
genomic: TTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTATGCAGgtattatact ... gcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagattttgcactgatatttggtcatatgactattgaaatgttgcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTTAACATGAATAAT
           cactgat  putative branch site (score: 3)
                                           ttgctttt  putative PPT
                                 tattgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaaatgaaaattgataagcctattttagaattcagattaaatttctagattttgcactgatatttggtcatatgactattgaaatgttgcttttacagGTCCTCACAGAACCAAAAAATGCTCTTGCTAAGCAGTACAAGAAATTATTTAACATGAATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- -aaatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcactg