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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggattaacatgtagagtcagtgtgaatgactgaaagagaatactaccgtatccttattttaacatttttgttttgtgtgttgctgttgacttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA

Basic information

species Glycine max
transcript GLYMA04G42840.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------tggattaa--catgtagagtcagtgtgaa--tgactgaaagagaatactaccgtatcctt--attttaacatttttgttttgtgtgt-----tgctgt-tga-cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
                                       | |   |   |||||     |||| || |  |||||  |  |      |||| |    ||  ||  |  | | | |      | | |     |  ||| ||| |||  |  |||| || || |||||||| || || ||| | || |||||||| ||||||| |||||| || ||||| ||||| |  |||||||| |||||||||||||| |
gtgagtccgaaaaattcagagcaacttcatactaaactgttgtccatctcatgtcattacagtttgcacctgactatagtatgcggttacctttgttttgcatactgtcctctatacaacatctataataatcttgtatgatctttctgcagGTCTTGAATGAGGATCTTCGACTCGTGCTCGGGCAGCAAGAACGGATGATCAATGGCGCAAATGTCTGGAACTGGCCAGTATCATATGACAAGCTTGGTA

upper sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------tggattaacatgtagagtcag--tgtgaatgactgaaagagaatacta-ccgtatccttattttaacatttttgttttgt-----gtgttgctgt-tgacttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
                                              |  ||| |   || ||  ||  | | |||  |  | | |  |  |||     | |      | | | |      |     ||  |  ||| |||  |  |  |||| || || ||||| |||||||| ||| | || ||||||||||||||||  ||||| || || || ||||| |  ||||| || |||||||||||||| |
gcaagtctcaaaattttcagagcaacttggtagtcactgatctccatgtcatctcatgttagcttgcaacttactacagtaaagttttttccgctgtttcacaccgtcgtctataagacatcaatggtaatcttgtatgatcttctgcagGTCTTGAATGAGGACCTACGGCTTGTGCTTGGGCAGCAAGAGCGGATGATAAATGGCGCGAACGTATGGAACTGGCCAGTGTCATATGACAAGCTTGGTA

upper sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G038487_T01 (Zea mays), 3'ss of exon 8
tggattaacatgtag-agtcagtgtgaatgactgaaagagaatactaccgtatccttattttaacatttttgttttgtgtgttgctgttgacttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
     |||  |  || | | |||||  |   | |   || | |  | | | |    | | || |||  | |  |   | | ||  || ||   |  |  |||| || |||||||| |||||||| ||  | || |||||||| ||||||| |||||| ||||| || ||||| |  || ||||| ||||||||||| ||| 
----gtaatttacaggaattagtgtagaatgcggctgga-attggttcagaaaatgt-tcttgacaaatctaat--atcttttcatggtggtcttgtgcagGTCTTGAACGAGGACCTACGGCTTGTTCTTGGTCAGCAAGAACGGATGATCAATGGCGCCAACGTCTGGAACTGGCCGGTATCATATGACAAGCTCGGGG

upper sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G038487_T03 (Zea mays), 3'ss of exon 8
-----tggattaacatg-tagagtcagtgtgaatgactgaaagagaatactaccgta--tccttattttaacatttttg-------ttttgtgtgttgctgttgacttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
     |   | ||  || || ||| | |   |   | |     ||||| |  | | |  |  ||     ||  || |||       |  | | | ||  || ||   |  |  |||| || |||||||| |||||||| ||  | || |||||||| ||||||| |||||| ||||| || ||||| |  || ||||| ||||||||||| ||| 
gcatgtcagtcaatgtgataaagtaatttacaggaattagtgtagaatgcggctggaattggttcagaaaatgttcttgacaaatctaatatcttttcatggtggtcttgtgcagGTCTTGAACGAGGACCTACGGCTTGTTCTTGGTCAGCAAGAACGGATGATCAATGGCGCCAACGTCTGGAACTGGCCGGTATCATATGACAAGCTCGGGG

upper sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G038487_T02 (Zea mays), 3'ss of exon 8
-tggattaacatg-tagagtcagtgtgaatgactgaaagagaatactaccgta--tccttattttaacatttttg-------ttttgtgtgttgctgttgacttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
 |   | ||  || || ||| | |   |   | |     ||||| |  | | |  |  ||     ||  || |||       |  | | | ||  || ||   |  |  |||| || |||||||| |||||||| ||  | || |||||||| ||||||| |||||| ||||| || ||||| |  || ||||| ||||||||||| ||| 
gtcagtcaatgtgataaagtaatttacaggaattagtgtagaatgcggctggaattggttcagaaaatgttcttgacaaatctaatatcttttcatggtggtcttgtgcagGTCTTGAACGAGGACCTACGGCTTGTTCTTGGTCAGCAAGAACGGATGATCAATGGCGCCAACGTCTGGAACTGGCCGGTATCATATGACAAGCTCGGGG

upper sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G44446.3 (Arabidopsis thaliana), 3'ss of exon 7
tggattaacatgtagagtcagtgtgaatgactgaaagagaatactaccgtatccttattttaacatttttgttttgtgtgttgctgttgacttattaa-agGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
                || |  ||  || ||  |||  ||    |    |      ||  | ||| | ||||||  |  ||| | |||    ||||   |||| |||||||| |||||||||||||| ||||| || ||||| ||||||   || || || ||  | |||||||| |||||  | ||||||||||| ||  
----------------gtaaaagtacatcac--aaatggatcgatcatcttcaaccatcgtcacagtcttgtttcttaagttaccgtttctatatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTAAACGGAGCAAACATATGGAATTTACCAGTTGCTTATGACAAGCTCGGAG

upper sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------tggattaacatgtagagtcagtgt----gaatgactgaaagagaatac--taccgtatccttattttaacatttttgttttgtgtgttgctgt-tgacttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
                                                 | ||||   |    ||   |||    | || |||       ||| |  ||   |||||    | |  | | | ||     | | ||| ||| ||| || ||  |||| || || |||||||||||||| ||  | || || ||||| ||||||   |  || || ||||||||||| | ||||||||| ||||||||||||||  
gtaaaatctccttcccactaatttcctcaagatgacatagtagcatgaagtttaaggcgctctgttcttgtatctgcattactctggttaaatgccatatgctatccaccctctctc-tatctgcacaatttcttgatgtgtgatttttttcagGTGTTGAATGAGGATCTACGGCTTGTACTTGGACAACAAGACCGGATGCTGATGGGGGCAAATGTGTGGAACTGCCCAGTATCATATGACAAGCTTGGAG

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|31457354|gb|CD399382.1|CD399382
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|16349020|gb|BI974615.1|BI974615
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|11412638|gb|BF424649.1|BF424649
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|31458888|gb|CD400916.1|CD400916
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|31461472|gb|CD403500.1|CD403500
EST:     TATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|9258726|gb|BE346873.1|BE346873
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|192303644|gb|FG994538.1|FG994538
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATTTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|16995987|gb|BM085359.1|BM085359
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|19053439|gb|BM732106.1|BM732106
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
EST: gi|7686535|gb|AW757183.1|AW757183
EST:     TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAG                         GTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC
genomic: TTAAGCATATTCCTTTTATGCAACATCTATGGAGATATTTTGCAGAGCAGgtagaatttt ... cttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgtatccttattttaacatttttgttttgtgtgttgctgttgacttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
         ttattttaacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggattaacatgtagagtcagtgtgaatgactgaaagagaatactaccgtatccttattttaacatttttgttttgtgtgttgctgttgacttattaaagGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - -acatgta
- - - - - - - - - - - -tgaatga
- - - - - - - - - - - - - - - ctgaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct