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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgcatcttattcttatattgattttttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG

Basic information

species Glycine max
transcript GLYMA10G28620.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G28620.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g22870.1 (Oryza sativa), 3'ss of exon 3
gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgcat---cttattcttatattgattttt---tgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG
                                                                                      | ||  |  | | |||| | |    |  ||| |  |   ||||    ||||| | || |||  | | |   |    || |||||  | ||| |||||||||||||||| |||||||| ||||||||||| |||||| | || 
--------------------------------------------------------------------------------------gtttgcgttc-gtctctcagtatacttgtgacattttggtgcaattgcttatccctaaattagtgtatccgttttgctgcagTCTCTTGCTAGGATGAACAAGAAGGACTCATGGCTGTTCTGGTGGACTCTGTACTTGACT

upper sequence: GLYMA10G28620.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g06700.2 (Oryza sativa), 3'ss of exon 3
gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgcatcttattcttatattgattttttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG
                                                                || | ||||   |   ||  |  | |     |||  | |    || | |   ||     |||     ||    | ||    ||   |   || | ||| |  | |||||||||||||| ||||| || ||||| ||||||||||| || ||| | || 
----------------------------------------------------------------gtttgtgcttgcttcaaatgtgacattg---ctg--tttaccgtcctaaacaatg---acttttgcattgacttgatggaaataact---ccgtacagGCTCTTGCTCGGATGAACAAAAAGGACTCGTGGCTGTTCTGGTGGACTCTTTACTTGACT

upper sequence: GLYMA10G28620.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G048117_T01 (Zea mays), 3'ss of exon 3
gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgcatcttattcttatattgattttttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG
                                                                            || |  | |   ||        | | | |||| | |     |  |   |||   |   || | |  |  || ||    |||| |||||  | ||||||||||||||||||||||||||||| ||||||||||| || ||| | || 
---------------------------------------------------------------------------gtctgtgcctgctttgcctgt--gatgttaattgtattcgtgtgtgaaattgttgcaggttgtaacttgaatgtt----ccctgcagTCTCTCGCTCGGATGAACAAGAAGGATTCATGGCTGTTCTGGTGGACTCTTTACTTGACT

upper sequence: GLYMA10G28620.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgcatcttattcttatattgattttttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG
                                        | |    | |||  |     |        |   |  ||||    | |   ||     || | ||  | | ||   | |   |  ||| ||  |  | |  | || ||  |||  |  | ||||| |||||||||||||||||||| || |||||||||||||||||||| || |||||| | 
----------------------------------------gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgt-gttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA

upper sequence: GLYMA10G28620.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0060g00830.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgcatcttattcttatattgat--tttttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG
        |  |||||  | ||   |||  |  |||   ||    | | ||| |  | |  |      |   ||||| | |        | |   || | |||| | || ||||  ||   |  |  ||| |   |  ||| || ||  || ||||   | |||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||| ||
-------gttggtattggcatttcataggacttttgttatg----agtttcttttcccttgatca---ccattgaatgaaatg-----ctgatggcttgttctggagtccttatgcatgaattttatcat-tgggtaatatctttatcattgttgctgatacagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG

upper sequence: GLYMA10G28620.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S6_365V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgca--tcttattcttatattgatttt---ttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG
                                                                   ||      ||      || | |  ||       ||  |||   ||  |  || | | |||||  | ||    | | |||| || |   |  |  || ||| | ||||      |||||||||| ||| | ||||| ||||||||||| ||||||||||| 
-------------------------------------------------------------------tccaagttattgagggattgatgtagtttctattcaaaatgaattcgtagtaagagattgcagatgttgacttaagattggttatggatgacgtctgcagACCTTGGAGACATTGAACAAGAAAGATGCTTGGCTATTCTGGTGGACGCTGTACCTTACT

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|192314171|gb|FK011543.1|FK011543
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|18719390|gb|BM523167.1|BM523167
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|193529860|gb|FK485709.1|FK485709
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|298168658|gb|HO009588.1|HO009588
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCT
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCT
EST: gi|192322592|gb|FK014713.1|FK014713
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|19348499|gb|BM893031.1|BM893031
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|192333423|gb|FK023952.1|FK023952
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|58025339|gb|CX712080.1|CX712080
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|192314172|gb|FK011544.1|FK011544
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|298163961|gb|HO013606.1|HO013606
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|298170569|gb|HO019193.1|HO019193
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
EST: gi|192326657|gb|FK017314.1|FK017314
EST:     TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAG                         TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG
genomic: TTAATGATCTGGGTGAGAGTGTTTGGAAATTTGAATGTCTTGACCACGAGgtaggtattc ... gcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttattgatacgtgcttgcatcttattcttatattgattttttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG
                                 tattgat  putative branch site (score: 3)
                                       ttttttgcccctcc  CT-rich tract
                     atcttattcttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgcatcttattcttatattgattttttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA