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

...ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

Basic information

species Glycine max
transcript GLYMA13G42800.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
ctttatgtctaca-tgattttgtg-cac-attttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| | ||  | |  |||   | |   || |  |  || |  || |  |    | ||    |   | | |||    ||| | | || ||| |  |  |  |||| || || || || | ||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||
ctgtgtgagttctctgaacctataatactacctgcttctgtatattttcaaatcatgagcatgaagctaatacc-atgttctcatattgtt--ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
ctttatgtctacatg-attttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttc--cagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
   | ||   |  || || |  |  |||||   ||     |    |    ||     |  |    |       || ||    || |  |  | | |||  ||| ||||| || |||||||||||||| |||||| |||| ||||||||||||||  ||||||||||||| ||||||||||| ||| ||||||| || ||| ||
---tttgctgatgtgcatctcatatacattcgattagatgtaatgtaccctttcgagttttatgtagtgacatattgttgcctgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
-------ctttatgtctacatg-attttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
       |  | | ||||| || || ||    | | |||||   | || | ||    || |  | | ||  |  |||||  |     | | || |   ||  |  ||| |||||||| || | ||||||||| ||||||||||| |||||||| |||||  |||| || |  || || || || ||||||||||| || |||||| ||
ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaat----ttgtgaacattgtgctgatttgctt----ctctttttcatttaattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
-------ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
        || ||||   |    |||| |    || || | |||   | | ||| |||||   || || | | |     |||   | |  ||| |  |   |  ||||||||| ||||| ||||||||||| ||||||||||||||||| ||||||||  | |||||||||||||| || ||||| ||||||||||| || ||||||
tgaatgagttaatgtg-gctgagttttttttggatcttatattttgctgcctgggtttattacta-tggtgatacc---atgtcctcactttgtt--ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
ctttatgtctacatgattttgtgcacatttttttt---ttaatttcatggttttatagatactgatcaaatttggatg-gtgttatgttgctcatatcttc-cagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
   ||||| | | ||||||    | ||| | || |   |||| |  |   |   ||   |    ||    |    ||   | |  |||  |   ||| | | ||| ||||| || || || |||||||| |||||| |||| ||||||||||||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
---tatgt-tgc-tgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 6
------ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttat-agatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
       |||    ||     || ||      ||  |    ||  ||  || ||  |||  | || ||||  |  ||        || |  |  | || ||  | || ||||| || || || |||||||| |||||| |||| |||||||| |||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
ttgctgatttgcacctcttatatcttaaatgtatgctgccattttttgtattgtcctattgggtagtgatatatattat------ttgtaatctttatttcaac-agTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
-ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcat-atcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
    |||  || || | |   |    ||  |  || || | |       ||| | |  | ||     ||    ||  | || | ||  |  | |     ||| ||||| || || ||||||||||| |||||||| ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| ||
ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatat--tcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctc----atatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
     | |   | |  |           ||  |  | |||||||    ||       | || |    |     ||||  |   | | ||    |  | || ||| || || ||||| || || || || |||||||||||| ||||||| |||||  ||||||||||||| || ||||| |||||||||||||| |||||  ||
----ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
-----ctttatgtctacatg-attttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
      ||  | || | | | |     ||   || ||   |  | ||  ||  ||| || |||| || ||   |    ||  | ||   |  || |||  |   ||||| |||||||| || || || || |||||| ||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| 
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttt---tctcttataatt---agCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
-----ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
       |  | |  | |  ||  |      |  || ||| |  | || |  ||   ||     |  | |||||| | || |    |||| |||      ||||| ||||| ||||| || |||||||| ||||||||||||||||| ||||||||| ||||||||||||| ||||| || |||||||||||||| |||||||||
gaaagactattatggaaacaatgctaatggtaacttgtttatt-tctcttatttgggtacgatttagtgaaattttgctgat----tgtttctctctctctccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

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|207847156|gb|GD820803.1|GD820803
EST:     GCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAA
genomic: GCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|207758381|gb|GD727307.1|GD727307
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|7686354|gb|AW757002.1|AW757002
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|208191779|gb|GD994625.1|GD994625
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|19936402|gb|BQ080848.1|BQ080848
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|207752398|gb|GD725819.1|GD725819
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|207701978|gb|GD683852.1|GD683852
EST:     GCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAA
genomic: GCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|21887329|gb|BQ740542.1|BQ740542
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|208327646|gb|GE119368.1|GE119368
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
           tactgat  putative branch site (score: 2)
                                             tatcttcc  putative PPT
                atcaaattt  TA-rich tract