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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTTTCTCCCGGATCTAATGGTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAGgtttgttatccttaaatctttcaggctatattttacgtaagagaatgcttcctggtttaccctctttggattcatgcttccgttttgcttgtagacaatg...

Basic information

species Glycine max
transcript GLYMA02G40900.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g08600.1 (Oryza sativa), 5'ss of exon 4
GAATTTTCTCCCGGATCTAATGGTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAGgtttg-----ttatccttaaatctttcaggctatattttacgtaagagaatgcttcctggtttaccctctttggattcatgcttccgttttgcttgtagacaatg
||||| || || |||||||||||||| ||||| || |||||||| ||||| |||||| |  | ||||||||||| ||     | || |||    |||||||  || |  | ||  |  |  |  |||  |   ||||    |     ||  ||        |  ||| || |     
GAATTCTCCCCTGGATCTAATGGTCGCATGACAACCATGGGTGTTTATGTGCGTGATCTTATACTTGGACAGgtctgcctcttcattctttgtgctttcagtatagaaataaccaataaacacactttttctcttacaaattaacagttgttgtgctaaagtatcttttaaa-----

upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G37370.2 (Arabidopsis thaliana), 5'ss of exon 4
GAATTTTCTCCCGGATCTAATGGTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAGgtttgttatccttaaatctttcaggctatattttacgtaagagaatgcttcctggtttaccctctttggattcatgcttccgttttgcttgtagacaatg
|| ||||| || ||||| ||||| || ||||| ||||||||||| ||||| ||||||||||| ||||||| |||  || |     || |||||        || |||  |     |||  ||||||      | ||| || ||||    |       || || | |      
GAGTTTTCACCAGGATCAAATGGACGGATGACGACAATGGGTGTTTATgtacgtgatttgctgcttggactggtgagtcac----aagtcttt--------atattagatggtcaaat-tttcctg-----tcttctgtgaattctccatggaaaactgatttttg------

upper sequence: GLYMA02G40900.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G37370.4 (Arabidopsis thaliana), 5'ss of exon 5
GAATTTTCTCCCGGATCTAATGGTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAGgtttgtta----tccttaaatctttcaggctatattttacgtaa---gagaatgcttcctggtttaccctctttggattcatgcttccgttttgcttgtagacaatg
|| ||||| || ||||| ||||| || ||||| ||||||||||| ||||| ||||||||||| ||||||| |||  || |    || ||| ||      | | |  |||   ||     | |||| || | |||   ||    ||| |  |       | |  |||  || |       
GAGTTTTCACCAGGATCAAATGGACGGATGACGACAATGGGTGTTTATGTACGTGATTTGCTGCTTGGACTGgtgagtcacaagtctttatattagatggtcaaattttcctgtcttctgtgaattctccatggaaaactgatttttggctgg----gcagacttggatgcatctg---

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|192304017|gb|FG995289.1|FG995289
EST:     GTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAG                         TATTATTTCGACACGTTGTTTCCTCGCATCCCTGTTCCTGTATTGCGGCAG
genomic: GTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAGgtttgttatc ... gctgttgcagTATTATTTCGACACGTTGTTTCCTCGCATCCCTGTTCCTGTATTGCGGCAG
EST: gi|9987823|gb|BE661931.1|BE661931
EST:     TCGAATGACTACCATGGGTGTATATGTCCCGTGATTTGCTTCTTGGACAG                         TATTATTTCGACACATTGGTTCCTCGCATTCCTGT
genomic: TCGAATGACTACAATGGGTGTATATGTCC-GTGATTTGCTTCTTGGACAGgtttgttatc ... gctgttgcagTATTATTTCGACACGTTGTTTCCTCGCATCCCTGT
EST: gi|254343401|gb|GR857105.1|GR857105
EST:     GTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAG                         TATTATTTCGACACGTTGTTTCCTCGCATCCCTGTTCCTGTATTGCGGCAG
genomic: GTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAGgtttgttatc ... gctgttgcagTATTATTTCGACACGTTGTTTCCTCGCATCCCTGTTCCTGTATTGCGGCAG
EST: gi|254318502|gb|GR832670.1|GR832670
EST:     GTCGAATGACTACA-TGGGTGTATATGTCCGTGATTTGCTTCTTGGACAG                         TATTATTTCGACACGTTGTTTCCTCGCATCCCTGTTCCTGTATTGCGGCAG
genomic: GTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAGgtttgttatc ... gctgttgcagTATTATTTCGACACGTTGTTTCCTCGCATCCCTGTTCCTGTATTGCGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTTTCTCCCGGATCTAATGGTCGAATGACTACAATGGGTGTATATGTCCGTGATTTGCTTCTTGGACAGgtttgttatccttaaatctttcaggctatattttacgtaagagaatgcttcctggtttaccctctttggattcatgcttccgttttgcttgtagacaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctctt