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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaagtgttgaaatggggcatggaagttccaagaatgtgctgtttgttgtgattggttttggttgttttctttactatgtgttgtttttgtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGATGGTCCAAGTTGGGCCAAATACATGTTGATCTCTGGTTCTCCTGATGAT

Basic information

species Glycine max
transcript GLYMA02G10730.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0146g00040.t01 (Vitis vinifera), 3'ss of exon 1
---gagaagtgttgaaatggggcatggaagttccaag--aatgtgctgtttgttgtgattggttttggttgtttt-ctttactatgtgttgtttttgtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGATGGTCCAAGTTGGGCCAAATACATGTTGATCTCTGGTTCTCCTGATGAT
    | ||  | | |||  |   ||| |  |  |  |    |||    ||   |   ||   |||   || |     |||| ||| | |  ||||  ||||||||||| |||||| || |||||||||||||||||||||||| || ||||| | || ||    |||||||||||||||||||  ||||||||||||||||     
atgaaaaaaagcttaaactgatgatgaatttggccggttgttgtaacattaagttctatcaatttgttttctgaggttttattattt-tacttttcatgatTGAAGAGGAATGGCAGCAGAGTCTATTTACAAAGAGAGATGTATTGCTGTGGACGACGGCGGGAGTTGGGCCAAATACATGTCTATCTCTGGTTCTCCTG-----

upper sequence: GLYMA02G10730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0010g04010.t01 (Vitis vinifera), 3'ss of exon 1
gagaagtgttgaaatggggcatggaagttccaag--aatgtgctgtttgttgtgattggttttggttgtttt-ctttactatgtgttgtttttgtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGATGGTCCAAGTTGGGCCAAATACATGTTGATCTCTGGTTCTCCTGATGAT
   ||  | | |||  |   ||| |  |  |  |    |||    ||   |   ||   |||   || |     |||| ||| | |  ||||  ||||||||||| |||||| || |||||||||||||||||||||||| || ||||| | || ||    |||||||||||||||||||  |||||||||||||||||||||
--aaaaagcttaaactgatgatgaatttggccggttgttgtaacattaagttctatcaatttgttttctgaggttttattattt-tacttttcatgattgaagAGGAATGGCAGCAGAGTCTATTTACAAAGAGAGATGTATTGCTGTGGACGACGGCGGGAGTTGGGCCAAATACATGTCTATCTCTGGTTCTCCTGATGAT

upper sequence: GLYMA02G10730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0146g00020.t01 (Vitis vinifera), 3'ss of exon 1
gagaagtgttgaaatggggcatggaagttccaag--aatgtgctgtttgttgtgattggttttggttgttttctttactatgtgttgtttttgtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGATGGTCCAAGTTGGGCCAAATACATGTTGATCTCTGGTTCTCCTGATGAT
 | |||  |  |||  |   ||| |  |  |  |    |||    ||   |   ||   |||   || |    |||  |   | |  ||||  |||||||||||||||||| || |||||||||||||| ||||||||| || ||||| |||| ||  | |||||||||||||||||||  |||||||||||||||||||||
taaaagcat--aaactgatgatgaatttggccggttgttgtaacattaagttctatcaatttgttttctgaagttttatcattttacttttcatgattgaagAGAAATGGCAGCAGAGTCTATTTACAAGGAGAGATGTATTGCTGTGGATGACGGCTCGAGTTGGGCCAAATACATGTCTATCTCTGGTTCTCCTGATGAT

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|193547347|gb|FK502866.1|FK502866
EST:     TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAG                         AGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
genomic: TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAGgtattgaatc ... gtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
EST: gi|207690614|gb|GD672084.1|GD672084
EST:     TTTGCTCTTGATTCGGCTATCGAAGAGCTTGTTCACCTCGGCATGCAAAG                         AGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTTCGGTGAATGA
genomic: TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAGgtattgaatc ... gtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
EST: gi|193584261|gb|FK541571.1|FK541571
EST:     TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAG                         AGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
genomic: TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAGgtattgaatc ... gtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
EST: gi|10234850|gb|BE803738.1|BE803738
EST:     TTTGCTCTTGATTCGGCTATCGAAGAGCTTGTTCACCTCGGCATGCAAAG                         AGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTTCGGTGAATGA
genomic: TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAGgtattgaatc ... gtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
EST: gi|208118265|gb|GD914210.1|GD914210
EST:     CTCTTGATTCGGCTATCGAAGAGCTTGTTCACCTCGGCATGCAAAG                         AGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTTCGGTGAATGA
genomic: CTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAGgtattgaatc ... gtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
EST: gi|193680326|gb|FK624834.1|FK624834
EST:     TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAG                         AGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
genomic: TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAGgtattgaatc ... gtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
EST: gi|208050180|gb|GD845459.1|GD845459
EST:     TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAG                         AGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
genomic: TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAGgtattgaatc ... gtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA
EST: gi|298194773|gb|HO043245.1|HO043245
EST:     TTTGCTCTTGATTCGGCTATCGAAGAGCTTGTTCACCTCGGCATGCAAAG                         AGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTTCGGTGAATGA
genomic: TTCGCTCTTGATTCGGCCATCGAAGAGCTTGTTCACCTCGGCATGCAAAGgtattgaatc ... gtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtgattggttttggttgttttctttactatgtgttgtttttgtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGATGGTCCAAGTTGGGCCAAATACATGTTGATCTCTGGTTCTCCTGATGAT
                                        tttttgt  CT-rich tract
                     ttttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagaagtgttgaaatggggcatggaagttccaagaatgtgctgtttgttgtgattggttttggttgttttctttactatgtgttgtttttgtgattgaagAGAAATGGCGGCGGAGTCTATTTACAAAGAGAGATGTGTTCCTGTGAATGATGGTCCAAGTTGGGCCAAATACATGTTGATCTCTGGTTCTCCTGATGAT

- - - tgttgaa
- - - - - - - - - gcatgga
- - - - - - - - - - - - - - -ccaagaa
- - - - - - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - -tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt