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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcccagatttcccctcgtgcgttgatttcagacagccccataccaatttctagggtttttattgatgttgcggtaacatatgtttgattgtattgctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG

Basic information

species Glycine max
transcript GLYMA11G08290.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 1
gtaatcccagatttcccctcgtgcgttgatttcagacagccc-cataccaatttc-tagggtttttattgatgttgcggtaacatatgtttgattgtattgctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG
            ||| || ||    | |    |   |  ||| || | | |||||   | | | | ||| |  |     |  | | | ||||   ||    |     ||  ||||||||||||||||| || ||||| || || |||||||| ||||| || ||||| || || ||||| || ||||| || ||||| ||||| ||||| || |
-----------gttcgccgcgcagctcgccgccctccctcccacagatcgatttcgccgagctctgattcacttatttatcgctttt-tttg--cgtggctcccctctccgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACTCGCCGTCGCGATTCCAGGCTCAGGCCGACGCCGTCAACCTCATCTGTG

upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G165926_T01 (Zea mays), 3'ss of exon 1
gtaatcccagatttcccctcgtgcgttgatttcagacagccccataccaatttctagggtttttattgatgttgcggtaacatatgtttgattgtattg-ctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG
                            |   ||  |  ||   | ||  ||||| |       |     | | |  ||||  || |   || || |||  |||| |   ||||| ||||||||||| || |||||||| ||||||||||| ||||| || ||| |||| || || || || || || || || || ||||| ||||| ||||
--------------------------gtacgacatgcgccctgctgccg-tttctcgctccgagaactccgatccc-taactaatctcccatcgtgttggttttcctttgcagGCAACGATGATCTGCATAGACAATTCGGAATGGATGCGGAACGGCGACTACGCTCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATCTGCG

upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 1
-----gtaatcccag--atttcccctcgtgcg---ttgatttcagacagccccataccaatttctagggtttttattgatgttgcggtaacatatgtttgattgtattgctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG
        |||| |   | |||| ||  |||     |  || |  | |     |  |   ||  |         |||   |||     | |   | ||| | | |    | ||||    |||||||| |||||||||||||||||||| ||||||||||| || || ||||| |||||  || ||||||| |||||||| ||||| || ||||| || || |
gtatgcctatcctatttacttccacttttgccattctatttcctaatatttatactctttttcttctttcacaaattagggttttctcaccgattattttaatttgcatcattctgattcagGCGACTATGATCTGTATCGACAATTCCGAATGGATGCGAAATGGCGATTATTCTCCCACTAGATTTCAGGCTCAAGCCGACGCCGTTAATCTTATCTGTG

upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S14_318V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaatcccagatttcccctcgtgcgttgatttcagacagccccataccaatttctagggtttttattgatgttgcggtaacatatgtttgattgtattgctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG
    |      ||| |  |  || |||||||  ||  ||| |  | |     |      ||||  | | |   |  | ||  | |      || ||| | | | ||  ||||||||| ||| |||| || ||||| || || |||||||| ||||| ||||| || ||| || | |||||||||||||| || ||| | || || || ||||
---gtttgtttttttcgttactgagttgattg-agggagcactgtgcgtgcat------ttttggtgggtagagttggaagctgttgaacgttatatgggtgtttt--acagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG

upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ17485 (Selaginella moellendorffii), 3'ss of exon 1
gtaatcccagatttcccctcgtgcgttgatttcagacagccccataccaatttctagggtttttattgatgttgcggtaacatatgtttgattgtattgctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTC---TCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG
                                                               ||      | ||| |     | |   |    |||    |  |    ||||||||||||||||| || |||||||| || |||||||| || || || |||| |||  |   | |||| ||  | ||||| || ||||||||||| || |   
--------------------------------------------------------------gtaagctcctcgcgatctttcacgccaggcc-tatcttctcttgtgccagGCGACGATGATCTGCATAGACAATTCCGAGTGGATGCGAAATGGGGACTACTATCCGACGAGTAGATTCCAGTCCCAAGCTGATGCTGTCAATCTTATCT---

upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ28815 (Selaginella moellendorffii), 3'ss of exon 1
gtaatcccagatttcccctcgtgcgttgatttcagacagccccataccaatttctagggtttttattgatgttgcggtaacatatgtttgattgtattgctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTC---TCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG
                                                               ||      | ||| |     | |   |    |||    |  |    ||||||||||||||||| || |||||||| || |||||||| || || || |||| |||  |   | |||| ||  | ||||| || ||||||||||| || |   
--------------------------------------------------------------gtaagctcctcgcgatctttcacgccaggcc-tatcttctcttgtgccagGCGACGATGATCTGCATAGACAATTCCGAGTGGATGCGAAATGGGGACTACTATCCGACGAGTAGATTCCAGTCCCAAGCCGATGCTGTCAATCTTATCT---

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|193722335|gb|FK656283.1|FK656283
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|151409810|gb|EV279618.1|EV279618
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|193548323|gb|FK505316.1|FK505316
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAAC--GGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|208055142|gb|GD852375.1|GD852375
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|193666070|gb|FK610519.1|FK610519
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAAC--GGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|14258768|gb|BG881676.1|BG881676
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|213600544|gb|DB960092.1|DB960092
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|208173744|gb|GD967201.1|GD967201
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|213605510|gb|DB970667.1|DB970667
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|298183378|gb|HO028591.1|HO028591
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|298165035|gb|HO011084.1|HO011084
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|193486749|gb|FK448384.1|FK448384
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCCTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|213596699|gb|DB964046.1|DB964046
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|207712448|gb|GD693842.1|GD693842
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|4283205|gb|AI440627.1|AI440627
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|208113075|gb|GD912450.1|GD912450
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|208054615|gb|GD850258.1|GD850258
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|193724280|gb|FK657540.1|FK657540
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAAC--GGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|207745371|gb|GD716327.1|GD716327
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|193302970|gb|FK266620.1|FK266620
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|298162986|gb|HO011719.1|HO011719
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|209715414|gb|BW684698.1|BW684698
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|193545854|gb|FK501309.1|FK501309
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAAC--GGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|207813620|gb|GD783287.1|GD783287
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
EST: gi|151397896|gb|EV267769.1|EV267769
EST:     CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG                         GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatcccag ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttttattgatgttgcggtaacatatgtttgattgtattgctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG
                                       ttgctttcttc  CT-rich tract
     ttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcccagatttcccctcgtgcgttgatttcagacagccccataccaatttctagggtttttattgatgttgcggtaacatatgtttgattgtattgctttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGAGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTCAATCTCATATGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA