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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtatcataatttgactcaagataatctgacattctgtattgatcattctgagttaacatattaggagatgctaacatgttgcatgttttgccatgttgctatcagCAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAGCAAAGCTACAAATGAGGCAAGAAGGAGCCATCAAGAGGGATAGAGCAATGGCATACT

Basic information

species Glycine max
transcript GLYMA15G02940.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G72670.1 (Arabidopsis thaliana), 3'ss of exon 3
gtggtatcataatttgactcaagataatctgacattctgtattgatcattctgagttaacatattaggagatgctaacatgttgcatgttttgccatgttgctat---cagCAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAGCAAAGCTACAAATGAGGCAAGAAGGAGCCATCAAGAGGGATAGAGCAATGGCATACT
| | ||| ||| || || | | | | || | | | ||||| |||| |||| ||||||||| ||| || | ||| | || |||||||||| || |||| | | ||||||| | | | |||||||||||||||||||||||||| ||||||||||| ||||| |||| |||
-----------------gtaatgattatcagatatggattttgggata----gaatgggactcgtgggaga--ctaa-atgt-atatgttttgcaatgatgtgttgttcagAAGGGTTGGTGTGATAGCCCGGGAAGTATCAATGAAGTGAGAACGAAGCTACAAATGAGGCAAGAAGGAGCAATCAAGAGGGAGAGAGCTATGGTATATG
















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|208270125|gb|GE069019.1|GE069019
EST:     AATTACTTGATGAGCATCGCAACCAAGCTGATCCTTTTAATCAAATTGAG                         CAAGGATGGTGTGATATTCCTGGAA
genomic: AATTACTTGATGAGCATCGCAACCAAGCTGATCCTTTTAATCAAATTGAGgtggtatcat ... ttgctatcagCAAGGATGGTGTGATATTCCTGGAA
EST: gi|208044653|gb|GD841077.1|GD841077
EST:     CATCGCAACCAAGCTGATCCTTTTAATCAAATTGAG                         CAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAGCAAAGCTA
genomic: CATCGCAACCAAGCTGATCCTTTTAATCAAATTGAGgtggtatcat ... ttgctatcagCAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAGCAAAGCTA
EST: gi|7685627|gb|AW756275.1|AW756275
EST:     AATTACTTGATGAGCATCGCAACCAAGCTGATCCTTTTAATCAAATTGAG                         CAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAG
genomic: AATTACTTGATGAGCATCGCAACCAAGCTGATCCTTTTAATCAAATTGAGgtggtatcat ... ttgctatcagCAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAG
EST: gi|208254790|gb|GE057384.1|GE057384
EST:     AATTACTTGATGAGCATCGCAACCAAGCTGATCCTTTTAANCAAATTGAG                         CAAGGATGGTGTGATATTCCTGGAA
genomic: AATTACTTGATGAGCATCGCAACCAAGCTGATCCTTTTAATCAAATTGAGgtggtatcat ... ttgctatcagCAAGGATGGTGTGATATTCCTGGAA
EST: gi|207776587|gb|GD747459.1|GD747459
EST:     ATTACTTGATGAGCATCGCAACCAAGCTGATCCTTTTAAATCAAATTGAG                         CAAGGATGGTGTGATATTCCTGGAA
genomic: ATTACTTGATGAGCATCGCAACCAAGCTGATCCTTTTAA-TCAAATTGAGgtggtatcat ... ttgctatcagCAAGGATGGTGTGATATTCCTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaacatattaggagatgctaacatgttgcatgttttgccatgttgctatcagCAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAGCAAAGCTACAAATGAGGCAAGAAGGAGCCATCAAGAGGGATAGAGCAATGGCATACT
                  tgctaac  putative branch site (score: 1)
 acatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtatcataatttgactcaagataatctgacattctgtattgatcattctgagttaacatattaggagatgctaacatgttgcatgttttgccatgttgctatcagCAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAGCAAAGCTACAAATGAGGCAAGAAGGAGCCATCAAGAGGGATAGAGCAATGGCATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA