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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgtacaattccaatgatacctgggagttaatttcatgatagtccattttatggctagcaaaggtaatgtataatgtttcttatgtatacttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA

Basic information

species Glycine max
transcript GLYMA02G17400.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
acgtacaattccaatgatacctgggagtta---atttcatgatagtccatt-ttatggctagcaaaggtaatgtataatgtttctta-tgtatacttttat-gcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
      | | | ||   ||  ||  | |||   | || || |    |  || ||||   |    |  | |||  || ||||| || | | | ||  ||| |   |||| ||||| |||||||| ||||| ||||| || |||| ||||||  | |||||||| || ||||| ||||||||||||||||| |||| ||   || | |
------agtacgaaaactagttgtaaattatgcaatttataaccagcagttgttatccatgatcattgaaatacattatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 27
acgtacaattccaatgatacctgggagttaatttcatgatagtccattttatggctagcaaa-ggtaatgtataatgtttcttatgtatacttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
              ||| |||    ||   |||| ||     |  |||||  |      |   |  | |  ||||| |     || |||   ||    ||||||||||| || || ||||| || ||| |||| |||| |||||| || |||||||||||||| || || || || || || || || | || | |  |||
-------------gtgagacc----agcacattttata----tttattttgagctctttacttgaaagttcataatctgatcaatttat---ttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAATGGAACGACCTATATGGCGAGGGCGGTTCGAGGAAGAAGAAAGCACTGA

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 27
acgtacaattccaatgatacctgggagttaatttcatgatagtccattttatggctagcaaaggtaatgtataatgtttc-ttatgtatacttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
                            |||       |  |||  ||  ||   |       ||||| | |  |  |   ||   |   ||| | |  |||||||||| ||| | |||||||| |||| |||||||| ||| ||  | |||||||||||||| ||||||||||| || || ||  | | || | | ||||
---------------------------gtaaaaatgctacggtcacttgcattattttgtcttgtaatctctgctcctgaatttaatggccttgtgtttagGTTTGTGCGAGTATATCATCGGATTCAAAAAATATGAATGAGCTCGTTCAATGGAACGACCTCTACGGAGAAGGCGGGTCGAGGCACAAGACACCGTTGA

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 26
acgtacaattccaatgatacctgggagttaatttcatgatagtccattttatggctag---caaaggtaatgtataatgtttcttatgtatacttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
|    |||      || |   |||  |  |  ||    ||| |   || | |   ||    |       | | ||||  ||  ||   |     || |||||||| ||||| || || || || || || ||||||||||  || ||||| |||||||||||  | || ||||||||||||||||| || | |  |||  | |
agaagcaaacatgttgtt--ttggccgacatattttcaataatattttctgtatttaaagtcctgcaagaagcataac-ttcattccatgattcttgatgcagGTATGTGCAAGCGTCTCTTCAGAATCTACAAATATGACCGAGCTACTGCAATGGAACGAATTATATGGAGAAGGTGGATCAAGGAAGAGGGCATCCCTCA

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|192302641|gb|FG996335.1|FG996335
EST:     CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAG                         GTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
genomic: CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAGgtatattaat ... ttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
EST: gi|7686624|gb|AW757281.1|AW757281
EST:     CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAG                         GTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
genomic: CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAGgtatattaat ... ttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
EST: gi|120497078|gb|EH225245.1|EH225245
EST:     CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAG                         GTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
genomic: CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAGgtatattaat ... ttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
EST: gi|8826443|gb|BE210173.1|BE210173
EST:     CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAG                         GTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
genomic: CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAGgtatattaat ... ttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
EST: gi|13788848|gb|BG651439.1|BG651439
EST:     CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAG                         GTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
genomic: CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAGgtatattaat ... ttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
EST: gi|254341441|gb|GR850654.1|GR850654
EST:     CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAG                         GTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
genomic: CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAGgtatattaat ... ttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
EST: gi|120496527|gb|EH224694.1|EH224694
EST:     CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAG                         GTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA
genomic: CTGACGTTCGTCCCTTAAAGATGGAGGATTTTAGATATGCACATGAGCAGgtatattaat ... ttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatggctagcaaaggtaatgtataatgtttcttatgtatacttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
                                          tactttt  CT-rich tract
                        tataatgtttcttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgtacaattccaatgatacctgggagttaatttcatgatagtccattttatggctagcaaaggtaatgtataatgtttcttatgtatacttttatgcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - -caattcc
- - - - - - - tgatacc
- - - - - - - - - - - - - - - - ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctagca