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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactatggaagcctatgtcagtgctaattacattccatttgaaacttatttgtgtttacatatttttcgttcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTTTTGGGAATGTTCTTAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC

Basic information

species Glycine max
transcript GLYMA14G00760.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 3
gtaactatggaagcctatgtcagtgctaattac---attccatttgaaacttatttgtgtttacatatttttcgt-tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTTTTGGGAATGTTCTTAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC
|| |     | | | | |   | ||||   |     |||    ||  |||  |  | |   || | ||  |  || |  |   |||||||||| || ||||| |||||||||||| |||||||| |||| || || ||||| |||||  | |||||||||||||||||||||||||||||||||||
gtgataccagtatcttctcata-tgctgtatgtgtaattgttcttttaacccaaatataacta-acatcatcagtgtggtgatcagCTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCTTTGGTAATGTGTTGAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC

upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 3
gtaactatggaagcctatgtcagtgctaattacattc-catttgaaacttatttgtgtttacatatttttcgttcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTTTTGGGAATGTTCTTAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC
        |  ||   ||   | |  |   | ||||  |||  ||    |     || |  |||   |   |    |    |||||||||  |||| || || || |||||| |||| ||| | || || |  ||||| || ||  | ||||||||||||||||||||||||||||| |||||
--------gtgag---atccgaatcttctctgcatttacatccgagctctgaacatggt--catggctgggggctgtt---agCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACTTTGGAAACGTCTTGAGTGCTAATTTGGGGCAAGCTCCTGCAAGGCAAGC

upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 3
---gtaactatggaagcctatgt-cagtgctaattacattccatttgaaacttattt---------gtgtttacatatttttcgttca--tctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTTTTGGGAATGTTCTTAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC
     | | |   || | | | | | | ||||   ||||||  | |     | |            |   | ||||     | |||     |   ||||||||| ||||| || ||||| |||||  |||| ||| | || || ||||| || || ||  | |||||||||||||| |||||||||||||| |||||
gtgacatccaaataatctttttttctgagctacgaacattctgtatctgtttcacccccaataacagcactgacatgagcatggttggggccgttagCTGCTCTGAAAAGAGCAAATGTGGATCCGGCCCTCGTGCAGGAGGTCTTTTTCGGAAACGTCTTGAGTGCTAATTTGGGACAAGCTCCTGCAAGGCAAGC

upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------------------------gtaactatggaagcctatgtcagtgctaattacattccatttgaaacttatttgtgtttacatatttttc---gttcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTTTTGGGAATGTTCTTAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC
                                                                                        ||   ||     || ||   | |    | |  | |  |||  |||   |   ||  ||| || || ||    ||  |  || ||| |||||||||||||| ||||||||| |||| |||||  ||||||| || ||||| |||||||| ||||| ||||| || || |||||||| ||||||||
gtcagtcaacctcctttttttgtttgtttgtttatccccattggtttattctcttttgcttcaaaatttatgggttttgatattttcataggcatttgcccccatccaatttgggactcaaattaattataaaagcaggagttcttaaatgttgttttgtgtcaacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCTTTGGAAATGTTCTCAGTGCAAATTTAGGACAGGCTCCTGCTAGACAAGC

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|16349042|gb|BI974637.1|BI974637
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|7478350|gb|AW666230.1|AW666230
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|9986217|gb|BE660325.1|BE660325
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|10843553|gb|BF066841.1|BF066841
EST:     CCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: CCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|209700566|gb|BW670310.1|BW670310
EST:     TACCCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|19269211|gb|BM885467.1|BM885467
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|16348094|gb|BI973689.1|BI973689
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|19935544|gb|BQ080482.1|BQ080482
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|120491397|gb|EH219564.1|EH219564
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|192312109|gb|FK003872.1|FK003872
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGAGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|37993878|gb|CF805624.1|CF805624
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|7926100|gb|AW832126.1|AW832126
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|192317815|gb|FK009407.1|FK009407
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGAGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|192312110|gb|FK003873.1|FK003873
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGAGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|192329988|gb|FK021574.1|FK021574
EST:     CAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: CAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|7233754|gb|AW569097.1|AW569097
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|13481409|gb|BG510752.1|BG510752
EST:     TACCCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|192302972|gb|FG996988.1|FG996988
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTACAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
EST: gi|19345910|gb|BM890790.1|BM890790
EST:     TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG                         CTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT
genomic: TACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatgg ... tcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacattccatttgaaacttatttgtgtttacatatttttcgttcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTTTTGGGAATGTTCTTAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC
 tgctaat  putative branch site (score: 2)
                                     tttttcgttcatct  putative PPT
                    ttatttgtgtttacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactatggaagcctatgtcagtgctaattacattccatttgaaacttatttgtgtttacatatttttcgttcatctgcagCTGCTCTTAAAAGGGCCAATGTTGATCCATCCCTTGTGGAAGAAGTATTTTTTGGGAATGTTCTTAGTGCTAATTTGGGGCAAGCTCCTGCAAGACAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA