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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtcaacttcctctatatttgttttcttgattatcaactatatatttgatccatgtacaaaattttgtccatctgcctttggatcctccttttatatcttttgatgccagtataggaacagtataattctactactttcttattttgggaggtttgacactgcattgtgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGCCAAGATAATGAAGAGGTCAGTGGTGATGAAGACAGTGAGGAGGAAGAAG

Basic information

species Glycine max
transcript GLYMA11G35600.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G05470.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgagtgtcaacttcctctatatttgttttcttgattatcaactatatatttgatccatgtacaaaattttgtccatctgcctttggatcctccttttatatcttttgatgccagtataggaacagtataattctactactttcttattttgggaggtttgacactgcattgtgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGCCAAGATAATGAAGAGGTCAGTGGTGATGAAGACAGTGAGGAGGAAGAAG
                                                                            |  | ||| | | |||  || |||  ||  |  || | | ||  |   | |  | |    |   ||  |   ||  |    ||| |   |||      ||| | |||||||||| |||||||| |||||||||||||||||||||||||||||  |    |||||||||||  | ||||||||||| |  || || || |||||||
---------------------------------------------------------------------------gtaagtctt-gtagcctttttctatgactagt--tgactgaatttgc-tacttcagtcactccttttcttcggttccgtgactttaatg-tgctacaacatttttagGTGAGTGAGCGTGATGACAAATTGCTTGCTGAGCACATGGCTAAGCTTAGAATGGATAATGAAGAAATGAGTGGTGATGAGGGAAGCGAAGATGAAGAAG

upper sequence: GLYMA11G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g07100.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtgtcaacttcctctatatttgttttcttgattatcaactatatatttgatccatgtacaaaattttgtccatctgcctttggatcctccttttatatcttttgatgccagtataggaacagtataattctactactttcttattttgggaggtttgacactgcattgtgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGCCAAGATAATGAAGAGGTCAGTGGTGATGAAGACAGTGAGGAGGAAGAAG
||||||||    ||  | ||    ||||| ||  | |      | |   | | ||| | | ||    || | | ||||  |||||      || ||  | | ||| | |       | |   | | |||   ||   | | ||||   ||    |  |||| ||      ||       |||||||||||| | ||||||||| | || |||||||| ||||| || || || || || ||||||||||| |||||||||||||     || ||||| ||||
gtgagtgttc-tttaatttaatcatgtttcctcaaatgctg--tttccctctcatctagggact---ttgttttcatcatccttt-----ttcattaaaaaccttctaa-----acacatctatattatttatcctgtccattctatattcttaaactttggcatattggtg-------cagGTGAGTGAAAGAGATGATAAACTACTAGCTGAGCATATGGCAAAACTTCGGCAGGACAATGAAGAGGTTAGTGGTGATGAAGGTGAGGAAGAGGAGGAAG

upper sequence: GLYMA11G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0067g01710.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtgtcaact-tcctctat----atttgttttctt---gattatcaactatatatttgatccatgtacaaaattttgtccatctgcctttggatcctccttttatatctt----ttgatgccagtata--ggaacagtataattctactactttcttattttgggaggtttgacactgcattgtgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGCCAAGATAATGAAGAGGTCAGTGGTGATGAAGACAGTGAGGAGGAAGAAG
|||||| ||||   || ||||     |||||||| |||      | | || | |  |  | |    |||      ||| |   |    | |  | | | | || ||| | |||    || ||   | | |   |  ||| || || |   |||  ||  |||  ||       |||    |     ||||||  ||||||||||||| || |||||| | ||||||||||| |||||||||||| | ||  | || || ||  ||||||| ||||||| |||||| || || ||||
gtgagtttcaatcatcttctacttaaatttgtttcctttcaatcttttaattctcaacctaacgtctgt-tggtttttggctaagtcacttcggaaactttctgttagaacttgctctttatttaattttgctgtcacattagaaattagctatctttatatcatgtc---cctgatgtggtgcattgattc--agGTGAGTGAACGGGACGATAAACTACTTGCTGAGCATATGGCTAAGCTAAGTCATCAGAACGAGGAAATCAGTGGCGATGAAGGCAGTGAAGAAGAGGAAG

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|51344772|gb|CO985505.1|CO985505
EST:     CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCA                         GTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
genomic: CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCAgtgagtgtca ... tgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
EST: gi|21602150|gb|BQ612481.1|BQ612481
EST:     CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCA                         GTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
genomic: CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCAgtgagtgtca ... tgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
EST: gi|192306826|gb|FK002996.1|FK002996
EST:     CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCA                         GTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGTTAAGCTACGC
genomic: CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCAgtgagtgtca ... tgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
EST: gi|254322253|gb|GR837667.1|GR837667
EST:     CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCA                         GTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
genomic: CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCAgtgagtgtca ... tgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
EST: gi|254323855|gb|GR840388.1|GR840388
EST:     CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCA                         GTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
genomic: CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCAgtgagtgtca ... tgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
EST: gi|208030362|gb|GD830724.1|GD830724
EST:     CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCA                         GTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC
genomic: CAATAGAACAACACAAGGGTAAACTTGTGGTTAAGGAGGCAGCTAGAGCAgtgagtgtca ... tgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataattctactactttcttattttgggaggtttgacactgcattgtgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGCCAAGATAATGAAGAGGTCAGTGGTGATGAAGACAGTGAGGAGGAAGAAG
                             gtttgac  putative branch site (score: 4)
                                                ttctc  putative PPT
          tactttcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtcaacttcctctatatttgttttcttgattatcaactatatatttgatccatgtacaaaattttgtccatctgcctttggatcctccttttatatcttttgatgccagtataggaacagtataattctactactttcttattttgggaggtttgacactgcattgtgattctcagGTGAGTGAACGTGATGATAAATTGCTTGCTGAGCACATGGCTAAGCTACGCCAAGATAATGAAGAGGTCAGTGGTGATGAAGACAGTGAGGAGGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG