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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG

Basic information

species Glycine max
transcript GLYMA11G14640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
gttaggagatt-tctttttcttctat-caatgagatggctgctgttttttgtgtttgttttaatagcgtgttcccca---cttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
|||||   ||| |||| ||||  | | |  ||| | | |||     | |    | | |      |   || | | ||     ||||  |   | || | || |  ||   | |  || ||| |   |  | || ||| | ||   | || || |  ||   |  |||||             |||| ||||       || ||||| | |||||| ||||| |||||||||||||| || ||||||||||| ||||||||||| || ||||| ||||| || ||||| ||||||||  | || |
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatg--cagtagctactg-cttaaacgttgttaagttac--aataaaaactgtat---aatgacaag-----------cttttctgttg------gtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 5
gttaggagatttctttttcttctatcaatgagatggctgctgtt-ttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
          ||  ||||  | |   | |   ||  ||  || | |||||         | | |      |||    |||    ||||   | |  || |||    |||  |   || ||       | |  |||||| |    |||   | |||  |  ||    | | | ||| ||| || |||   |       ||||| |  ||||| ||||| ||||| |||||||| || || |||||||||||||| ||||| || ||||| || || || ||||||||||||||||| || |
---------gttagtttttatttgctatttccat--ctcttgctattttgaacaaaacatgaaattcatatccttttttgtaaatgtttgttctgtagcttt----attcaccattgacaaagaacatac--aataacatattcata---taattctactga----agtaaccttgtttcttgtgtgcta-------cagGTGTTCTTTAAGGATGTAGCTGGCTGTGATGAAGCCAAACAAGAAATTATGGAATTTGTTCATTTCCTGAAAAATCCCAAGAAATATGAAGAACTGGGAG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 5
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaat--aacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                                                                                  ||||| |   | || ||   |   ||| ||   |  |  |    | ||| ||  || | ||  ||  ||   || |     |||| | ||       |||| || |       || ||||| | |||||| ||||| || |||||||| || || || |||||||| ||||||||||| || ||||| || ||||| ||||| ||||||||  | || |
----------------------------------------------------------------------------------ttgttgtagcttcattt---gcccttttcttaagaaacaaagcatactacatgaaattcgaagatttgtcttttcat----caatgtctac------ttttctgctg------gtccagGTGTTTTTTAAGGATGTAGCCGGTTGTGACGAAGCAAAACAAGAAATAATGGAGTTTGTGCATTTCCTTAAAAACCCTAAGAAGTATGAAGATTTGGGAG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                                                                                                      ||||    ||        ||||  |||    |   ||   ||| | | | |||   |   |    | | |||  |||| ||||||  | ||   ||| | ||||| || ||||||||||| ||||| ||||| || |||||||||||||||||||| || ||||| |||||||||||||| ||||||||  | ||||
------------------------------------------------------------------------------------------------------gttagagactt------agagttttgcc---tttgtttttaatga-tccgtttggaattta----taaacttacttttgttgttt--tcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgc-taaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                                                                                                   |  |   ||   ||  ||  |    | ||  | |  | ||| |     | |||||          | ||||| || ||  | | | ||   |||||  ||| | ||||||||||||||||| || || || ||||| || |||||||||||||| ||||| || |||||  ||||||||||||||||||||||  | || |
--------------------------------------------------------------------------------------------------gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagattta-ctactgatctattttgttttttgc-cagATATATTTTAAAGATGTTGCGGGATGCGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 5
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
|||||   |   || |||||| | ||||  || ||| |  | |||  | ||     |  ||||   | ||  |    | |  |  ||||  |  |    ||| | |  |     |   |  | |     |        |||| || | ||  | | |     | ||||  |  | | | | || ||  |  | || ||||||| ||| |||||||||||||| |||||||| || ||||||||||| ||||| ||||| |||||||||||||| || || |||||||||||  | || |
gttagctaa---ctgtttcttttgtcaa--aggtggtttgtctttagtttgcagcatccaata---tttttacagtatacaataattattatatcctccttgctcacctatggttataatcattcgattttctctctctgactatta-ttattattatcattattattgtttgtttatctatttttggacctagtacagGTCTTTTTCAAAGATGTTGCTGGATGTGATGAAGCAAAGCAAGAAATCATGGAATTTGTTCACTTCCTCAAGAATCCTAAAAAATATGAAGAGTTGGGAG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 6
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                                                                          | ||     ||  | | |  |   | |||  || | |   ||| |     | |||              ||  ||   ||| | |     | | |           ||| ||| ||  |   |||||    || |||||||||||||||||||| ||||| || ||||| ||||||||||| || |||||  | || ||||| ||||| ||| | ||||| ||||
-------------------------------------------------------------------------aagttataagtgggaacatgtcgcgtatggccatgtacatttggtacagtagttgc--------------atttgtctttttgaaaagaggtgtat-----------tttatttgatcct-cacagGTAATGTTCAAAGATGTTGCTGGTTGTGACGAGGCAAAACAAGAGATTATGGAGTTCGTTCACTTTTTGAAAAACCCCAAGAAGTATCAGGAACTTGGTG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S456_6V6.1 (Physcomitrella patens), 3'ss of exon 6
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgtt-cagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                                                                                                 |    | |  |    | ||   || | |||  |          | ||| |   | |   || |  |   |||   || |  | | | | |  | |  || |||||    || ||||||||||| |||||||| ||||| || ||||| ||||||||||| || |||||  | |||||||| ||||| ||  ||||||| ||||
----------------------------------------------------------------------------------------------ggatgagagatgctgttccatgat-ggtgagctatttg-----ccaataatgaagacgtactaggggtagagttttgtttttgatgtatctgttgtgtcattacagGTTATGTTCAAAGATGTTGCCGGTTGTGACGAGGCAAAACAAGAGATTATGGAGTTCGTTCACTTTTTGAAGAACCCCAAGAAGTACCAAGAACTTGGTG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S39_149V6.1 (Physcomitrella patens), 3'ss of exon 5
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagtt-catttaagagacaatatttatcttcttttttttgtttcattttgtt-cagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                                                                                                                                               ||   ||     |    || |||        | | |||| ||  |  | ||| | |||||    || ||||||||||||||||| || ||||| || ||||| || ||||| ||||| |||||| | ||||| || ||||||||| ||||||| || |
--------------------------------------------------------------------------------------------------------------------------------------------gtgatgtcttatgactcccggaaaatgacggagctttattttgtgcgttgtgttgctgcagGTGATGTTCAAAGATGTTGCTGGTTGCGACGAGGCAAAACAAGAGATCATGGAATTTGTTCACTTCTTGAAGAATCCCAAGAAATATCAAGAACTTGGGG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ31204 (Selaginella moellendorffii), 3'ss of exon 6
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                                                                                                                                 ||  || ||  |||     ||  |||       |    ||      || |   ||    | ||||  ||||||  ||| || ||||| ||||||||||| || || ||| ||||  ||||||| |||||||||||||| ||||| || ||||| || |||||||| || |
--------------------------------------------------------------------------------------------------------------------------------gtatgtagct--acagcttctttgtttc-----tagcggttgatcaattgtgcctga---aatttg--cagGTCACTTTCAATGATGTCGCTGGTTGTGACGAAGCCAAGGAAGAGGTTATGGAATTTGTCCACTTCCTGAAGAATCCCAAGAAGTACGAAGAACTTGGCG

upper sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17143 (Selaginella moellendorffii), 3'ss of exon 5
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                                                                                                                                 ||  || ||  ||| | | ||  |||           ||||||       || ||  | |  || | ||||||  ||| || ||||| ||||||||||| || || ||| ||||  ||||||| |||||||||||||| ||||| || ||||| || |||||||| || |
--------------------------------------------------------------------------------------------------------------------------------gtatgtagct--acagttactttttttctagcg----gtttatcaa-----ttgtgcctgaaatt-tgcagGTCACTTTCAATGATGTCGCTGGTTGTGACGAAGCCAAGGAAGAGGTTATGGAATTTGTCCACTTCCTGAAGAATCCCAAGAAGTACGAAGAACTTGGCG

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|192302548|gb|FG994842.1|FG994842
EST:     TCAACATAGGAAAAGCCCATACTAAAGTAGACAAAAATGCCAAAAACAAG                         GTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATG
genomic: TCAACATAGGAAAAGCCCATACTAAAGTAGACAAAAATGCCAAAAACAAGgttaggagat ... ttttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG
                      tttatcttcttttttt  CT-rich tract
                  aatatttatcttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC