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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttcctttcatttgcaaatattgtgtttctaattttagagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC

Basic information

species Glycine max
transcript GLYMA08G23990.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 12
----gtatgctttcctttcatttgcaaatattgtgttt-ctaattttagagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC
     | |  | || ||  |  |    |||||||   | | |||   | | ||| ||  | |  |||  | ||   | ||||||| |||||||| || ||| | |||||||| || |||||||| ||||| |||||||||||||| ||||| ||||| || |||||||| || |||||||
gtatatctcttctcattctaaatttgcatattgttcatacaaatcggacatttgatctgattgtttc--tcataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC

upper sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 11
gtatgctttcctttcatttgcaaatattgtgtttctaattttagagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC
                                        || |  |   || ||  ||| |||| |   || ||||||| ||||| ||||| ||||| ||||||||| | ||||||||  | |||||||||||||||||| | || || || || ||||||||||| |||||||
---------------------------------------gtttggttcaatctaa--aatacaataaa-atttagGTTCTGATGGATTTTCCTCAACTGACAATGACACTGCCTGATGGGAGAGAAGAATCTGTCATGAAGAGAACTACGCTCGTAGCTAACACTTCTAACATGC

upper sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
--------gtatgctttcctttcatttgcaaatattgtgtttcta-attttagagttggtcaaactaattcaatga-ttgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC
         | |  | || ||||| |   ||  | |  ||||  | || || ||| |  | || | |  | | ||| || |||||||||| ||||| ||||| ||| | || |||||| | |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||||| ||||
gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC

upper sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------------------------------------------------------------------------------------------------gtatgctttcctttcatttgcaaata---ttgtgtttctaattttagagttggtcaaactaattcaatgat--tgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC
                                                                                                       ||  | |  ||   | ||  ||||   |  | ||||      | |  |      ||||  |  |    |  |||  |||| |||||||| ||||| || || |||||||| |||||||||||||||||||| ||||| ||||||||||| || || ||||| ||||| ||||||||||
gtgtggtcttgcctggacaattttcttgaagcatgggtttcaattttataacaatgtgtattgctgttgttaaaacttgtgcattatcaagttgtcttgctacatcatatttttgagtgtggtaatacgataatatttcatgccatggtatgtagttaactgttggagctgtggtgtgtagGTACTAATGGATTTTCCACAGCTGACAATGACCTTACCTGATGGTCGTGAAGAGTCTGTTATGAAGCGTACCACTCTCGTGGCCAACACCTCAAACATGC

upper sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------------------------------------------------------gtatgctttcctttcatttgcaaatattgtgtttctaattttagagttggtcaaactaattcaatgat--tgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC
                                                                                              ||  | | ||   | |  | ||||  |||  | || || ||||    |   |||  |  ||   |  |  |||  |||| || ||||| ||||| ||||| || ||||| ||||| || ||||| || || || |||||||||||||| || || ||||| ||||| ||||||||||
gtttcgtaatgtgaccataacttccttgctcgtaatcaaattgttcatctttgcggatgtttacgaatctgactcagggattcttcctattgcagtggggtatctcatgaact-caaagtttgcttctccaaatttatg--taaccaatttgtttggcttgtggtgtgtagGTGCTGATGGATTTTCCACAACTGACGATGACCTTACCCGACGGTCGGGAGGAGTCCGTCATGAAGCGTACTACGCTTGTGGCCAACACATCAAACATGC

upper sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 10
gtatgctttcctttcatttgcaaatattgtgtttctaattttagagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC
            |   ||    ||| |    ||| |    |||   ||| |   || ||| ||    |||  |||||  | |  |||||||| || ||||| || ||| | |||||||| || ||||| |||||||||||||||||||| || || ||||| |||||||| ||||
-----------gtcggttctagaatttcccattttt---cttatctttgtttctacaaat-cacctcttg--cagGTGTTGAAAGACTTTCCACAGCTTACTATAACACTTCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGC

upper sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 11
gtatgctttcctttcatttgcaaatattgtgtttctaattttagagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC
            |   ||    ||| |    ||| |  | |     ||   ||||  |  ||     |||  |||||  | |  |||||||| || ||||| || ||| | |||||||| || ||||| |||||||||||||||||||| || || ||||| |||||||| ||||
-----------gtcggttctagaatttcccatttttcttatcttgtttctacaaatcacctc-----ttg--cagGTGTTGAAAGACTTTCCACAGCTTACTATAACACTCCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGC

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|19935049|gb|BQ080079.1|BQ080079
EST:     ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAG                         GTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA
genomic: ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAGgtatgctttc ... gattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA
EST: gi|16278104|gb|BI942728.1|BI942728
EST:     ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAG                         GTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA
genomic: ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAGgtatgctttc ... gattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA
EST: gi|151402942|gb|EV272755.1|EV272755
EST:     ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAG                         GTTCTAATGGACTTTCCCCAACTCACAATGACATTACCTGATGGTCGTGAA
genomic: ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAGgtatgctttc ... gattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA
EST: gi|18692695|gb|BM521543.1|BM521543
EST:     ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAG                         GTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA
genomic: ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAGgtatgctttc ... gattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA
EST: gi|21889244|gb|BQ742457.1|BQ742457
EST:     ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAG                         GTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA
genomic: ATGCCGTTGTTTATGTCGGCTGTGGGGAACGTGGAAATGAAATGGCAGAGgtatgctttc ... gattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatattgtgtttctaattttagagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC
                                 aactaat  putative branch site (score: 2)
         tgtttctaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttcctttcatttgcaaatattgtgtttctaattttagagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC