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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaacatttggatgaattcttcaaggggtttctgtttaaatgagatgtttattgtgatttttctttattttctattttgttaatttatttgttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATGCGAGCTTATGGAGTTCAGTTTAAAGAAGGGCCAGATGGTTTTGGAGTGT

Basic information

species Glycine max
transcript GLYMA15G16830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G16830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G20130.1 (Arabidopsis thaliana), 3'ss of exon 2
ccaacatttggatgaattcttcaaggggtttctgtttaaa----tgag-atgtttattgtgatttttctttattttctattttgttaatttatttgttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATGCGAGCTTATGGAGTTCAGTTTAAAGAAGGGCCAGATGGTTTTGGAGTGT
      |    |||| ||||    |  ||  || |  | |    || | || |   |  |   |    || ||||    ||||  |  ||| ||| |||  |||| ||||| | || ||||| ||||||||||| ||||| ||||| |||||| || |||||||||||||| ||||||||||||| |||||||||||||| || |
----ggtacaaatgagttctaacggcagtaactttagacaattctgtgcatttccctcatatgtgagattgatttagggtttttgtcttttgtttcttca-ctagCTGGAGACAGCAGATCCGGATTTCTACAAAATTGGCTATGTTCGAAGTGTGAGAGCTTATGGAGTTGAGTTTAAAGAAGGTCCAGATGGTTTTGGTGTCT

upper sequence: GLYMA15G16830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 2
ccaacatttggatgaattcttcaaggggtttctgtttaaatgagatgtttattgtgatttttctttattttctattttgttaatttatttgttcctcta--gTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATGCGAGCTTATGGAGTTCAGTTTAAAGAAGGGCCAGATGGTTTTGGAGTGT
| |||  || | | |  | ||   |   |  |  ||| || |   || || ||||  ||||| |  || |||| || | || |||| |  | |  || |  ||||||||| || || ||||||||||||||||| || ||||| || ||| | ||||| || || ||| | || || |||||||| ||||| |||||||| |
caaacgatttgtttatctgttttggaaatagccctttgaaggcattgatttttgt--tttttttcaatcttcttttgtttttatttttgagattatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTTCGAGCATACGGTGTTGAATTCAAGGAAGGGCCTGATGGATTTGGAGTCT
















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|7691132|gb|AW759265.1|AW759265
EST:     CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAG                         TTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
genomic: CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAGgtaaattcca ... gttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
EST: gi|15286356|gb|BI470247.1|BI470247
EST:     CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAG                         TTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
genomic: CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAGgtaaattcca ... gttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
EST: gi|7691176|gb|AW759308.1|AW759308
EST:     CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAG                         TTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
genomic: CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAGgtaaattcca ... gttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
EST: gi|22539829|gb|BU089672.1|BU089672
EST:     CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAG                         TTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
genomic: CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAGgtaaattcca ... gttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
EST: gi|151409002|gb|EV278810.1|EV278810
EST:     CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAG                         TTGGAGCCCGCTGACCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG
genomic: CATTTCCCCTGTTTCAGCCTCCCCAAGTTGAAGAGACAACATCGTCTGAGgtaaattcca ... gttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttattgtgatttttctttattttctattttgttaatttatttgttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATGCGAGCTTATGGAGTTCAGTTTAAAGAAGGGCCAGATGGTTTTGGAGTGT
                                tgttaat  putative branch site (score: 3)
                                      tttatttgttcctct  CT-rich tract
     attgtgatttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaacatttggatgaattcttcaaggggtttctgtttaaatgagatgtttattgtgatttttctttattttctattttgttaatttatttgttcctctagTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATGCGAGCTTATGGAGTTCAGTTTAAAGAAGGGCCAGATGGTTTTGGAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
ccaacat
- - - - - - tgaattc
- - - - - - - - - - - - ggggttt