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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcctatttcaagttttttggcagcagtttatggaatagctttcacccattctatctcagaagaagtctttagtgtttacaaacatgttagattttgagaatgaaatctgtagttagtacacgtgttcaaaactcatcatgatgtaaataagactcattttccttaatccactttattcagGTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAAGAAGAGGGGGGATGTTCATAAATTCATGTTTTGCTCATTGCCAGAGTGA

Basic information

species Glycine max
transcript GLYMA20G29930.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G29930.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g40290.1 (Oryza sativa), 3'ss of exon 9
gttcctatttcaagttttttggcagcagtttatggaatagctttcacccattctatctcagaagaagtctttagtgtttacaaacatgttagattttgagaatgaaatctgtagttagtacacgtgttcaaaactcatcatgatgtaaataagactcattttccttaatccactttattcagGTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAAGAAGAGGGGGGATGTTCATAAATTCATGTTTTGCTCATTGCCAGAGTGA---
                                                                             |||   | || |||||||      |  |    | |      |    |  |||||   |  |  |  |    | |    |||   | || ||||    |    ||||  | |||  ||  ||| |    ||| |||  |||||| |    |||  |    | |  ||||||||||||||||| |||||||| ||||||||||||||   
----------------------------------------------------------------------------attattcagat-ttagattccattgaacaggcatatgtgagatttctggattcaag--ttgttgtcttcgtgacattcttcagagttctgaatctgtctg---cagGACTCAGGAATGCAATGTTGACGGCTCTGAAGCCGTTCCA---AAATGAACAGGGTGTAGGGATGTTCATAAATTCTTGTTTTGCACATTGCCAGAGTGAGCT

upper sequence: GLYMA20G29930.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0050g00570.t01 (Vitis vinifera), 3'ss of exon 10
gttcctatttcaagttttttggcagcagtttatggaatagctttcacccattctatctcagaagaagtctttagtgtttacaaacatgttagattttgagaatgaaatctgtagttagtacacgtgttcaaa-actcatcatgatgtaaataagactcattttccttaatccactttattcagGTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAAGAAGAGGGGGGATGTTCATAAATTCATGTTTTGCTCATTGCCAGAGTGA
                                                                             |||   | | |  |    || || |  |  | || ||||  || |  | || ||  |  |||  || |  |        | |||    | |||   | || |||||||||||||   || ||||||  ||||||||  |  |||||||   ||||||||||||| |||||||| ||||||||||| |||||||||||||| |||||
--------------------------------------------------------------------------caattaagtagaaggaaaccattaagtaatatttatgaagtt--taaaaattttaaagtatccattttggtcca-------tttattactttcaattttcgttgttcagGTTTTAGGAAAGATATGCTTACAGCTTTGAACCAATTCTATACTTATTCAAGAAGAGGAGGGATGTTTATAAATTCATGCTTTGCTCATTGCCAAAGTGA
















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|51336923|gb|CO980789.1|CO980789
EST:     CAAGGCGAACCTGGCGGAGTGTACAGCAGACCAAATTGATACACTGCAAG                         GTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAA
genomic: CAAGGCGAACCTGGCGGAGTGTACAGCAGACCAAATTGATACACTGCAAGgttcctattt ... ctttattcagGTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAA
EST: gi|151413033|gb|EV282841.1|EV282841
EST:     CAAGGCGAACCTGGCGGAGTGTACAGCAGACCAAATTGATACACTGCAAG                         GTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAA
genomic: CAAGGCGAACCTGGCGGAGTGTACAGCAGACCAAATTGATACACTGCAAGgttcctattt ... ctttattcagGTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaaactcatcatgatgtaaataagactcattttccttaatccactttattcagGTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAAGAAGAGGGGGGATGTTCATAAATTCATGTTTTGCTCATTGCCAGAGTGA
                                   ccttaat  putative branch site (score: 4)
                                         tccacttt  CT-rich tract
               atgtaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcctatttcaagttttttggcagcagtttatggaatagctttcacccattctatctcagaagaagtctttagtgtttacaaacatgttagattttgagaatgaaatctgtagttagtacacgtgttcaaaactcatcatgatgtaaataagactcattttccttaatccactttattcagGTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAAGAAGAGGGGGGATGTTCATAAATTCATGTTTTGCTCATTGCCAGAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG