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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATCGTGTCATCGGAACCCTACTCGGCTCCGTCCTTCCCGATGGAACCGTCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcactttcttttttactattaattgttaattcattattatcaataataattttagtatatatttgttagccgctgctatacatatgaggagttta...

Basic information

species Glycine max
transcript GLYMA11G35020.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G35020.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os05g01450.2 (Oryza sativa), 5'ss of exon 1
CGATCGTGTCATCGGAACCCTACTCGGCTCCGTCCTTCCCGATGGAACCGTCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcactttcttttttactattaattgttaattcattattatcaataataattttagtatatatttgttagccgctgctatacatatgaggagttta----
 || || |||||||| ||||| |||||||||||||| ||||| || |||||| || ||||||| ||||| |  || || |||||||| ||   ||| |||||     ||| |   | |  || ||     |     |   || ||||    ||   ||  ||  | ||  |     | | |  |  |  ||      | |    
GGAGCGCGTCATCGGCACCCTCCTCGGCTCCGTCCTCCCCGACGGCACCGTCCATGTCCGCAACTCCTACGTCGTCCCCCACAACGAGTCCCCCGACCAGgtaa---actataaatatctctcttctccttccgcccggcatcatcagatctagggttt-tacttcttcttccattgattccctgaacttgcctttctaatgtt

upper sequence: GLYMA11G35020.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os05g01450.1 (Oryza sativa), 5'ss of exon 1
CGATCGTGTCATCGGAACCCTACTCGGCTCCGTCCTTCCCGATGGAACCGTCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcactttcttttttactattaattgttaattcattattatcaataataattttagtatatatttgttag--ccgctgctatacatatgaggagttta-
 || || |||||||| ||||| |||||||||||||| ||||| || |||||| || ||||||| ||||| |  || || |||||||| ||   ||| |||||     |      | | |  | |   |        ||| || |    ||    |||   | |   |   ||    ||       | | | |     ||| | 
GGAGCGCGTCATCGGCACCCTCCTCGGCTCCGTCCTCCCCGACGGCACCGTCCATGTCCGCAACTCCTACGTCGTCCCCCACAACGAGTCCCCCGACCAGgtaaactataaatatctctcttctccttccgcccggcatcatcagatctagggttttacttcttcttccattgattccctgaacttgcctttctaatgttaag

upper sequence: GLYMA11G35020.1 (Glycine max), 5'ss of exon 1
lower sequence: AT2G39990.1 (Arabidopsis thaliana), 5'ss of exon 1
CGATCGTGTCATCGGAACCCTACTCGGCTCCGTCCTTCCCGATGGAACCGTCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcactttcttttttactattaattgttaattca--ttattatcaataataattttagtatatatttgttagccgctgctatacatatgaggagttta-------------------------------------------------------------------------------------
 || || ||||||||||| || ||||| ||  || | || || ||||||||||||||||||||||| || || || |||||||| |||||   ||| |||||||   | |||  | | ||   ||      |   ||   |   ||||  |    ||  |||   || |||  |||| |  | | | | | | ||||  | |                                                                                     
TGAACGAGTCATCGGAACTCTCCTCGGATCTATCTTACCTGACGGAACCGTCGATATCCGCAATTCATACGCCGTCCCTCACAATGAATCATCCGATCAGgttcgaaattttgatctctaaatttctcctctctctcgattctctatcgttggagatcctag---atctttcgtagctgaagatttgcttgttaggatgtgaatgtttataggagtagtgttagcttcataccccaaggttgtgacttgtgataagttttgagggttatggtttgatatggatgcag

upper sequence: GLYMA11G35020.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0019g03470.t01 (Vitis vinifera), 5'ss of exon 1
CGATCGTGTCATCGGAACCCTACTCGGCTCCGTCCTTCCCGATGGAACCGTCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcactttctttttta--ctattaattgtt--aattcattattatcaataataattttagtatatatttgttagccgctgctatac-atatgaggagttta
||| || |||||||||||||| ||||| ||  ||  ||||||||| ||||| ||||| |||||||| || |||||||||||||| || ||   ||| |||||   |   | |||||  ||   |||   || ||    || ||| || | |    |  |||| | || | ||| ||          || | || ||| || |   
CGAGCGAGTCATCGGAACCCTCCTCGGTTCGATCTCTCCCGATGGCACCGTAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgtttttctctttgctaaattatcgcttttttgggttaatttttgttag--gttgtttttggatttttttttttttttaattcatgcgatgtgaagaat---

upper sequence: GLYMA11G35020.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ10683 (Selaginella moellendorffii), 5'ss of exon 1
CGATCGTGTCATCGGAACCCTACTCGGCTCCGTCCTTCCCGATGGAACCGTCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcactttcttttttactattaattgttaattcattattatcaataataattttagtatatatttgttagccgctgctatacatatgaggagttta
 ||||| || || || || || || || ||  |      |||||||||  ||||||| |||||||| ||||||||||| |||||||| ||    || |||||            | |||  |  |    ||  |||   |  | | |||     ||  | |  |                                    
AGATCGGGTGATTGGGACGCTGCTGGGGTCGATTTCCAGCGATGGAACGATCGATATTCGCAATTCTTATGCTGTTCCGCACAACGAGTCGTCTGATCAGgtc---------ggtatttgatcctggaagtggatt---tcgtgtaaatcgggtttccaatgcag-----------------------------------

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|208260565|gb|GE058145.1|GE058145
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|19348580|gb|BM893112.1|BM893112
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|298194162|gb|HO040810.1|HO040810
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|11687319|gb|BF594959.1|BF594959
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|151396266|gb|EV266143.1|EV266143
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|192324837|gb|FK015348.1|FK015348
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|193376019|gb|FK339990.1|FK339990
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|192297073|gb|FG992009.1|FG992009
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|7235195|gb|AW570524.1|AW570524
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|208280005|gb|GE079643.1|GE079643
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|298183586|gb|HO028799.1|HO028799
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|193679783|gb|FK623969.1|FK623969
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCAACCAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCA-CCAAAA
EST: gi|8283050|gb|BE020611.1|BE020611
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|193402058|gb|FK368411.1|FK368411
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|21677106|gb|BQ629457.1|BQ629457
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|298176963|gb|HO023324.1|HO023324
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|208277548|gb|GE079539.1|GE079539
EST:     CGATATCCGCAATTCCTATGCTGTTCCTTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: CGATATCCGCAATTCCTATGCTGTTCC-TCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|208112903|gb|GD908862.1|GD908862
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|4313745|gb|AI460864.1|AI460864
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         N
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccag-
EST: gi|4313745|gb|AI460864.1|AI460864
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         N
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccag-
EST: gi|298189337|gb|HO037740.1|HO037740
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|37997123|gb|CF808712.1|CF808712
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|209724854|gb|BW672637.1|BW672637
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
EST: gi|207711128|gb|GD694081.1|GD694081
EST:     TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAG                         GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA
genomic: TCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcact ... ttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATCGTGTCATCGGAACCCTACTCGGCTCCGTCCTTCCCGATGGAACCGTCGATATCCGCAATTCCTATGCTGTTCCTCACAACGAATCTATCGAACAGgttcttcactttcttttttactattaattgttaattcattattatcaataataattttagtatatatttgttagccgctgctatacatatgaggagttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT