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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatttaatataattagacttagtgtacttttcactttgctgtttctttttttcttgcaaatagtgcttaactgagccaattttggtcaaatgaatgtaagGGTACTAATGAAGTGAGACGAAGGTCTAGATTCTTACGTAGAAGAGGAAGAGTTCGTCGATTGAAGTACACCTGGAAATCTGCTGCTTATCATTCAATTA

Basic information

species Glycine max
transcript GLYMA01G39490.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39490.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G157820_T02 (Zea mays), 3'ss of exon 10
gttaatttaatataattagacttagtgtacttttcactttgctgtttctttttttcttgcaaatagtgcttaactgagccaattttggtcaaatgaatgta--agGGTACTAATGAAGTGAGACGAAGGTCTAGATTCTTACGTAGAAGAGGAAGAGTTCGTCGATTGAAGTACACCTGGAAATCTGCTGCTTATCATTCAATTA---
               || ||   | |||     | | |||| || | |||   |||  ||   ||   ||||| |  |    | |||  |   |  ||||   ||||||||   ||  || |   ||| || ||||  ||  | ||  |||| | ||| ||||| ||||||||||||||||||||||| | |||  |||  |  |   
--------------gttggatgcactgtgaccctta-tttgttgatacttacattcaagccggtaa--cttaatttgg----tgttgtccgtgttgatgtcccagGGTACT---GAGTTGCGCACAAGATCAAGATATTTTAGAAGGCGAGGTAAAGTCCGTCGTTTGAAGTACACCTGGAAATCTGCAGGTTACAATTTCAAAAGGA

upper sequence: GLYMA01G39490.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G23380.1 (Arabidopsis thaliana), 3'ss of exon 10
gttaatttaatataattagacttagtgtacttttcactttgctgtttctttttttcttgcaaatagtgcttaactgagccaat--tttggtcaaatgaatg-taagGGTACTAATGAAGTGAGACGAAGGTCTAGATTCTTACGTAGAAGAGGAAGAGTTCGTCGATTGAAGTACACCTGGAAATCTGCTGCTTATCATTCAATTA
     | || ||  | || || |  |  |||||    ||| |   ||| |  |    |  |  || | ||   | ||   |||  ||| ||     || |    ||| || |||  |||||||  ||||||| |||||  ||||||| ||||| | ||| || || |||||||| |||||||| |||||||| |||||||||||||
----gtatattaacactaaacctttttgactttg---tttacaaattcctgataaaatcgatttatttctcttcggatttaatgctttagtttctggactaaccagGTTAATAACCAAGTGAGGAGAAGGTCAAGATTTCTACGTAGGAGAGGCAAAGTGCGGCGCTTGAAGTATACCTGGAAGTCTGCTGCATATCATTCAATTA

upper sequence: GLYMA01G39490.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 8
gttaatttaatataattagactta-gtgtacttttcactttgctgtttctttttttctt--gcaaatagtgcttaactgagccaattttggtcaaatgaatgtaagGGTACTAATGAAGTGAGACGAAGGTCTAGATTCTTACGTAGAAGAGGAAGAGTTCGTCGATTGAAGTACACCTGGAAATCTGCTGCTTATCATTCAATTA---
|||| |   || |  ||   ||||  |  |  ||  |     |  || |||  ||      |||  |  |  || | |      | |||           | |        ||||||||| ||| |||| || ||||| ||||| ||  | || |||||||| || |||||||| || ||||||||||| | ||| ||||||||||   
gttagt---atttttttgtgcttatatacatattgtatcggacccttccttccttgacaaggcatttttttttttattttttggaatttctattttctcgtttctttagGGTAATGAAGTAAGAAGAAGATCAAGATTTTTACGCAGGCGGGGTAGAGTTCGCCGCTTGAAGTATACTTGGAAATCTGCCGGTTACCATTCAATTAGGA

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|254327702|gb|GR834667.1|GR834667
EST:     CTGGTCCTCCTGGGGATGTTGCAAATTCCCTCATGGACGGCTATTCCAAG                         GGTAATAATGAAGTGAGACGAAGGTCTAGATTCTTACGTAGAAGAGGAAGA
genomic: CTGGTCCTCCTGGGGATGTTGCAAATTCCCTCATGGACTGCTATTCCAAGgttaatttaa ... tgaatgtaagGGTACTAATGAAGTGAGACGAAGGTCTAGATTCTTACGTAGAAGAGGAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcttgcaaatagtgcttaactgagccaattttggtcaaatgaatgtaagGGTACTAATGAAGTGAGACGAAGGTCTAGATTCTTACGTAGAAGAGGAAGAGTTCGTCGATTGAAGTACACCTGGAAATCTGCTGCTTATCATTCAATTA
                   gcttaac  putative branch site (score: 3)
                                          aaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatttaatataattagacttagtgtacttttcactttgctgtttctttttttcttgcaaatagtgcttaactgagccaattttggtcaaatgaatgtaagGGTACTAATGAAGTGAGACGAAGGTCTAGATTCTTACGTAGAAGAGGAAGAGTTCGTCGATTGAAGTACACCTGGAAATCTGCTGCTTATCATTCAATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT