Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtgctgcttgattctcccgccccaaaaaagactcttttgctgcttgatttgtacatgaaaatgagtagtcatagattttggcatcagttcttgtttcaaaaaatatttaatttgatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG

Basic information

species Glycine max
transcript GLYMA02G46380.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 6
gtaagttgtgctgcttgattctcccgccccaaaaaagactcttttgctgcttgatttgtacatgaaaatgagtagtcatagattttggcatcagttcttgtttcaaaaaatatttaatttgatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG
                                                             |||  |     |  |     ||| |    ||     ||| ||        |||| | |  ||    ||| | ||  || |||||||| |||||||||||||| || |||||||||||||| || || || ||||| || || || || |||
-----------------------------------------------------------gtatgctagcctttccttcccaattatattctctaaatttgatttgc----catttcactgaatagtgtat-ttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG

upper sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 8
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttgtgctgcttgattctcccgccccaaaaaagactcttttgctgcttgatttgtacatgaaaat-gagtagtcata---gattttggcatcagttcttgtttcaaaaaatatttaatttgatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG
                                                   | | | |||     || | ||||  |   |   ||||   || |  | |||  | |||  |  |  |||| |||    |||   || |  ||||||||||| ||||||||| |||| |  ||||  |||||||| ||||| || ||||||||||| ||||| |||
--------------------------------------------------gtaagtagtattcctaatttgagttcttgcatgtgattagagcctacggtctcatatcagtacctccttaaattg----atttcatcatgcagATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAG

upper sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 8
gtaagttgtgctgcttgattctcccgccccaaaaaagactcttttgctgcttgatttgtacatgaaaatgagtagtcatagattttggcatcagttcttgtttcaaaaaatatttaatttgatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG
                                     | | ||||| |||||||  | |   || || ||  |  |  || | ||    |    | ||||  |                   ||||||   | ||  ||||||||| |||| ||||||||||| |  |||| ||||||||||||||| | |||||| ||||| |||||||||
----------------------------------gttagtgttttgatgcttgagatttctctgtaattggatcattgtatactt----actcatccttgagt-------------------tgaatttcatgctgcagATATGGTCAGTCTTTCCCTGTTTCAGAGGAAGCTCTTGATTCCAGTTTCTCCCTTCCAATAGGGAAAGCAAAG

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|7041702|gb|AW471543.1|AW471543
EST:     GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|7028855|gb|AW458638.1|AW458638
EST:     GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|192295237|gb|FG986956.1|FG986956
EST:     GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|11273897|gb|BF324286.1|BF324286
EST:     CTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: CTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|21887778|gb|BQ740991.1|BQ740991
EST:     GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcatcagttcttgtttcaaaaaatatttaatttgatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG
                                             tgtcctct  CT-rich tract
          ttcttgtttcaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtgctgcttgattctcccgccccaaaaaagactcttttgctgcttgatttgtacatgaaaatgagtagtcatagattttggcatcagttcttgtttcaaaaaatatttaatttgatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG