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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttatcatattagcactgtaacaccaacatattctcttgaagttacttgagtctttttgtttgattatgtgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA

Basic information

species Glycine max
transcript GLYMA06G45160.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
------------gtttttatcatattagcactgtaacaccaacatattctcttgaagttacttgagtctttttgtttgattatgtgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA
            ||| || |   | ||  | |    |  |||     |||        | || |    | |   | |||   ||  | ||| || |  |||||||||||| ||||| |||||||| ||||| |||||||| |   | || |||||||| ||  | ||  | ||||   | ||  | | | |  ||   | | 
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaat--gcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
gtttttatcatatta-gcactgtaacaccaacatattctcttgaagttacttgagtctttttgtttgattatg---------tgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA
   || | ||||  | | ||  |   ||  |||| |          ||| |  | | ||  | || ||| |||         ||||     |   ||||||||||||| |||||||||||||| ||||| || || ||||   | || |||||||| ||  | ||  |  |||   | ||  | | |     ||      
aggttcaacatagcatggacattcttacatacatttcaatcgtttcttagtcaaattttcattttagatcatgaccattgattgctcactcaacatgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATGAAACATGCCTT

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gtttttatcatattagcactgtaacaccaacatattctcttgaagttacttgagtctttt-tgtttgattatgtgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAA-CATGGCACTTACA
       |||  ||   | | | |  |   |  ||| || ||||   |||| ||| |    |  ||||     |  ||  |     |||||||||| || |||||||||||||| ||||| ||||||||||   | |||||||| ||  |||| ||  ||||||  || ||  | |||   |||   |   |
------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctt-tttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTG-TGGTA

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------gtttttatcatattagcactgtaacac-caacata--ttctcttgaagtt------actt-------gagtctttttgtttgattatgtgcttttaaatt-ttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGC-ACTTACA
                                                           ||   | |||  |    ||||  ||  || ||||   |||||| |||||      | |        |||   |||||    ||||| || | | || || || ||||||||||| |||||||||||||| ||||| || |||||||   | ||||| ||||| ||  | ||  | |||| |   ||  | | | |  || || ||  
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattat-tgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG-

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 11
----------------------------------------------------------------gtttttatcatattagcactgtaacaccaacata---ttctcttgaagttacttgagtctttttgtttg------------attatgtgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA
                                                                    | ||||||  | | | |  |   ||   |    |  ||||  | ||| |    ||||| ||||              |||| || || |   |  |||||||||||||| ||||| |||||||| ||||| || |||||||   | || |||||||| ||  |  |  |  | |   ||||  | | |       |||   
gttggttgaatctgttctttgttcaataaatcctccatcatacagtttgagaaaaaaaaagcaatccgtcatcatag-aacccagggatctcattgtgcattattcttccatttattgagttctttatgttcttcacacctgaccattaagttctctctcaacttgcagCAAGTATACATGTATTTCCGTGGAAGTGGAAAAGCTGCAGAGATTAAACGTGAGGCAGCACGTAGTGCTCTAAGTTCAGCCTTCTGATGAACATCTTTTT

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 11
-------------gtttttatcatattagcactgtaacaccaacatattctcttgaagttacttgagtctttttgtttgattatgtgctt--ttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA
              ||| ||     |  ||  | || | ||| ||  ||||  || |    ||||  |  || |   |   | ||| ||   |   | | |||||||||| || ||||||||||| |||||||||||||||  ||   |||||||||| || || ||||||||  | |||  |||  | | |  || |||  |  
gttcagtagtctgatttctagttcttctgc-ttctatctccagcac-ttctactgca---tcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG

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|162286177|gb|FC456625.1|FC456625
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGT
EST: gi|193337386|gb|FK303760.1|FK303760
EST:     CTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: CTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|31474417|gb|CD416445.1|CD416445
EST:     GATTTGNCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGT
EST: gi|209724206|gb|BW658112.1|BW658112
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|22928614|gb|BU545753.1|BU545753
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|9899156|gb|BE608183.1|BE608183
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|193318264|gb|FK285828.1|FK285828
EST:     GGTTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGT
EST: gi|192320764|gb|FK013854.1|FK013854
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|209700002|gb|BW661218.1|BW661218
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|213608211|gb|DB974909.1|DB974909
EST:     GATTTGGCCTTTGCCATCTCGAGTCAGTGCTGAGCATGTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|254347258|gb|GR853507.1|GR853507
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|209712375|gb|BW671227.1|BW671227
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|209723674|gb|BW662569.1|BW662569
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|15284739|gb|BI468630.1|BI468630
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
EST: gi|31459116|gb|CD401144.1|CD401144
EST:     GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG                         CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT
genomic: GATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttatca ... aattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttgaagttacttgagtctttttgtttgattatgtgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA
                          gtttgat  putative branch site (score: 5)
                     tttttgtttgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttatcatattagcactgtaacaccaacatattctcttgaagttacttgagtctttttgtttgattatgtgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC