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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtacaatgccattgacacctgggagttaatttcatgagagtccattttatggccagcaagggtagtgtataatgtttcatatgtatgcatttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA

Basic information

species Glycine max
transcript GLYMA10G02410.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
-atgtacaatgccattg-acacctgggagttaatttcatgagagtccattttatggccagcaagggtagtgtataatgtttcatatgtatgcatttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
  |    ||     ||| | |    | | || ||  |  |    |    |  |||  ||   |   ||   |||  || |   | ||||||  | | |  |||| ||||  ||||| || ||||| ||||| ||||||||||||||  | |||||||| || ||||| ||||||||||||||||| |||| ||   || | |
agtacgaaaactagttgtaaattatgcaatttataaccagcagttgttatccatgatcattgaaa-tacattatgttgctaactttgtatgtttgt-tatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA

upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 27
atgtacaatgccattgacacctgggagttaatttcatgagagtccattttatggccagcaag-ggtagtgtataatgtttcatatgtatgcatttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
              ||| |||    ||   |||| ||     |  |||||  |  |   |   |  |||  ||||| |     || |||  |      ||||||||||  || || ||||| || ||| |||||||||||||||| || |||||||||||||| || || || || || || || || | || | |  |||
-------------gtgagacc----agcacattttata----tttattttgagctctttacttgaaagttcataatctgatcaatttatttacc---acagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAATGGAACGACCTATATGGCGAGGGCGGTTCGAGGAAGAAGAAAGCACTGA

upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 27
atgtacaatgccattgacacctgggagttaatttcatgagagtccattttatggccagcaagggtagtgtataatgtttcatatgtatgcatt-tatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
                            |||       |  |||  ||  ||           ||| | | |  |  |  || |    || || | |  |||||||||  ||| |||||||||| |||| ||| |||||||| ||  | |||||||||||||| ||||||||||| || || ||  | | || | | ||||
---------------------------gtaaaaatgctacggtcacttgcattattttgtcttgtaatctctgctcctgaatttaatggccttgtgtttagGTTTGTGCGAGTATATCATCGGATTCAAAAAATATGAATGAGCTCGTTCAATGGAACGACCTCTACGGAGAAGGCGGGTCGAGGCACAAGACACCGTTGA

upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 18
---atgtacaatgccattgacac---ctgggagttaatttcatgagagtccattttatggccagcaagggtagtgtataatgtttcatatgtatgcatttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
      |||||  | |   |||     |     |||| |  |  |   | |||| | ||     |  | | ||  | |     |     | ||  |  |   ||||||||| |  || || ||||| || ||  |||||||||| || || ||||||||||||||||| ||||| ||||| || || || || | || | |  |||
acctactacaagtctacaaacatacattcttgtttaagtctacaaacatacattct-tgttt--ctggagcagcatcttgatctcttcctttacccgct---gcagGTTTGCGCGAGCGTTTCATCCGACTCGGCAAACATGAACGAGCTTCTCCAATGGAACGACCTGTACGGTGAAGGCGGGTCGAGGAAGAGGAAAGCGCTGA

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|14010976|gb|BG725898.1|BG725898
EST:     CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAG                         GTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
genomic: CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAGgtatattagt ... atttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
EST: gi|7234672|gb|AW570007.1|AW570007
EST:     CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAG                         GTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
genomic: CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAGgtatattagt ... atttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
EST: gi|24205678|gb|BU964931.1|BU964931
EST:     CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAG                         GTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
genomic: CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAGgtatattagt ... atttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
EST: gi|23064134|gb|BU578907.1|BU578907
EST:     CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAG                         GTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
genomic: CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAGgtatattagt ... atttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
EST: gi|9901539|gb|BE610507.1|BE610507
EST:     CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAG                         GTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
genomic: CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAGgtatattagt ... atttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
EST: gi|14010966|gb|BG725888.1|BG725888
EST:     CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAG                         GTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
genomic: CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAGgtatattagt ... atttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
EST: gi|33389718|gb|CA852925.1|CA852925
EST:     CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAG                         GTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
genomic: CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAGgtatattagt ... atttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
EST: gi|58023725|gb|CX710466.1|CX710466
EST:     CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAG                         GTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA
genomic: CCGACATTCGTCCCTTAAAGATGGAAGATTTTATATATGCACATGAGCAGgtatattagt ... atttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatggccagcaagggtagtgtataatgtttcatatgtatgcatttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
                        tataatgtttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtacaatgccattgacacctgggagttaatttcatgagagtccattttatggccagcaagggtagtgtataatgtttcatatgtatgcatttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - -caatgcc
- - - - - - - - acacctg
- - - - - - - - - - - - - - - - -tcatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - -gccagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgc