Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagctatttatcctcttctaaatagtttcactgtttcacaacatcaagtctgaacagctagaaagtatacaaagaagctataagaactaacagaaaataatctaatgttgtcttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTTTCCGGGTTGTATAACTAAAATCTTCTGTGAACCCAGAGCTAATTGAAAT

Basic information

species Glycine max
transcript GLYMA04G42010.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatagctatttatcctcttctaaatagtttcactgtttcacaacatcaagtctgaacagctagaaagtatacaaagaagcta-taagaactaacagaaaataa-tctaatgttgtcttaat-tgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTTTCCGGGTTGTATAA--CTAAAATCTTCTGTGAACCCAGAGCTAATTGAAAT
                      |   |    | || ||  |     |||    |  | ||  |||    | ||        |  |  | ||  | ||  |||   |||  |  ||| | | | |  ||||||||| ||||||||||||||||| ||| |||||| |||||||   || |||||  |||| ||    | | | ||| | || |   |       || ||  
-------------------gtaaggcaaaacctctcttcta----gtcagagatttaaagacagagcaaacaccttttgtttggtttgtacacatagttaattgctctgcttatgtttgattctatagGTCTTCAATGGAAGAGACACTACAAGGATCTGAAGAGGATAGCTAGTTCATTCCGCATTGTTTAGACTTTAGAACTTTTTTGGATATATCAGATCTTCAA--

upper sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g15360.t01 (Vitis vinifera), 3'ss of exon 4
gtatagctatttatcctcttctaaatagtttcactgtttcacaacatcaagtctgaacagctagaaagtatacaaagaagctata----agaactaacagaaaataatctaatgttgtct-taattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTTTCCGGGTTGTATAACTAAAAT-CTTCTGTGAACCCAGAGCTAATTGAAAT
       |||  | | ||||        | ||| || |||| | ||  ||    |||  | |||  | || |  |||    | |     | ||| | |   || ||||   | |||   | |   |||||||||||| ||||||||||| ||||| ||||| || ||||||||||| |||||||| ||||| ||    | ||  |||| ||||   || |   ||  | | 
------gtatagaacttcttt---gctctctca-tgcttcatatcaaaaaacaagaattgttagcca-taaatgaagtttttgtctcgcaaaacgagctataactaattataggttacttatttctgcagGTCTTCAATGGAAGAGACATTACAAGGATTTAAAAAAGATAGCTGACTCTTTCCGTGTTGTCTAGTCGAGATATTTCTATGAATTGAGGGAGCATAAATA-
















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|31308568|gb|CD393771.1|CD393771
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
EST: gi|15285767|gb|BI469658.1|BI469658
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
EST: gi|5509839|gb|AI856397.1|AI856397
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
EST: gi|209716367|gb|BW657487.1|BW657487
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
EST: gi|192314016|gb|FK011108.1|FK011108
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTTTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
EST: gi|31469528|gb|CD411556.1|CD411556
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
EST: gi|31561437|gb|CD487275.1|CD487275
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
EST: gi|213604484|gb|DB983516.1|DB983516
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
EST: gi|105633575|gb|DW246938.1|DW246938
EST:     TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCG                         GTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT
genomic: TGCCACTGCAGCTGGCAACCGCTTATATTTGTTTGGAGTAACAGGCAGCGgtatagctat ... ttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaaagaagctataagaactaacagaaaataatctaatgttgtcttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTTTCCGGGTTGTATAACTAAAATCTTCTGTGAACCCAGAGCTAATTGAAAT
                                        ttgtctt  CT-rich tract
                          aaaataatctaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagctatttatcctcttctaaatagtttcactgtttcacaacatcaagtctgaacagctagaaagtatacaaagaagctataagaactaacagaaaataatctaatgttgtcttaattgcagGTCTTCAGTGGAAGAGACACTACAATGATTTGAAGAAGATAGCTGAATCTTTCCGGGTTGTATAACTAAAATCTTCTGTGAACCCAGAGCTAATTGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT