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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataacccttattcttatttgtttcataatcgtttgatatttaattagaaagttatgcatcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT

Basic information

species Glycine max
transcript GLYMA13G27600.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
aataacccttattcttatttgtttcataatcgtttgatatttaattagaaagttatgcatcttctaaatttgacatggtattt-tcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT
 | |||   ||  |    || ||  |  ||  ||  ||| ||  |  | |   | |    | | ||   ||      | ||   |||| |    |   |||| ||||| || ||||| || |||||||||||||| || |||||||||||||||||||||||||| ||||| || || |||||||| || || ||||||||
-agaacatgtaagcgctgttattctagcattattgaataatttttatgcataatttaatccctttactcttattcctgaatccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT

upper sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 2
aataacccttattcttatttgtttcataatcgtttgatatttaattaga----aagttatgcatcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT
      ||  | |  || ||  |      | |  || | |||| ||  |    ||||  | || | |   |||   |  |     | | |  ||   |   |||| |||||||| ||||| || ||||||||||| || || |||||||||||||| ||||||||||| || || || || ||||| || || |||||||||||
-tcgctccagacttataattactattaggttgcatgctgtttatttgcatctcaagtgcttcacccttataataaaaacttactctctttcttt---tttccagATTTGGATTTTCTGTTCCACATGTTTTTTCTCGCACGATACTGCAAGCTTCTGGAGGAGAACTCATTTAGAGGAAGAACTGCCGACTTTTTTTACATGCT

upper sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G112609_T01 (Zea mays), 3'ss of exon 2
--aataacccttattcttatttgtt-tcataatcgtttgatatttaattagaaagttatgcatcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT
  |  |  ||  | |  || ||  | | |  || | ||  | |||| ||  |   ||     |  |  |   ||   |||      |  | ||       |||| |||||||| || || || ||||| |||||||| || |||||||||||||| ||||| ||||| || || || || |||||||| || |||||||||||
gcatcattccagacttataattactgttagcattgcttactgtttatttgca---tttcaagtgcttcacccttataatgaagacctactctttttcccccagATTTGGATTTTCTATTCCACATGTTCTTTCTTGCACGGTACTGCAAGCTTCTGGAGGAAAACTCATTTAGAGGAAGAACTGCTGACTTTTTTTACATGCT

upper sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G21810.1 (Arabidopsis thaliana), 3'ss of exon 2
aataacccttattcttatttgtttcataatcgtttgat--atttaattagaaagttatgcatcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT
  |   ||||    |   | ||   ||  ||  |  |   ||||| ||     || ||   |  |   ||  |||| || | || |  |      |  ||||| ||||| ||  |||| |||||||||||||| ||||| |||||||| || || || || ||||| |||||||| | ||| || |||||| ||||||||||
--tgctccttgacatctctagtactatgctccctgtaaggatttattttctttgtgattgttaattagaagctgacttgttcttgttatcaatcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT

upper sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------aataacccttattcttatttgtttcataatcgt---ttgatatttaattagaaagttatgc---atcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT
                                                                    | | ||| |  || |    ||  ||    |    || || ||  | | |  ||| ||    ||    |   | | |     ||| |  ||   |     | ||| ||||| ||| |||| |||||||| ||||| || || |||||||| || ||||| || ||||| |||||||| | ||||||||||||| | ||||||||
gtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttgtcacattattagctctaggctgctacttgttaatagcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT

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|192308645|gb|FG999726.1|FG999726
EST:     ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG                         ACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
genomic: ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGGgtaaaatttc ... gaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
EST: gi|192327521|gb|FK018197.1|FK018197
EST:     ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG                         ACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
genomic: ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGGgtaaaatttc ... gaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
EST: gi|298194426|gb|HO041074.1|HO041074
EST:     ATATCAGTTTTGGCGTCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG                         ACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCCCGTTACTGCAAGCTTC
genomic: ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGGgtaaaatttc ... gaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
EST: gi|192319097|gb|FK010633.1|FK010633
EST:     ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG                         ACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
genomic: ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGGgtaaaatttc ... gaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
EST: gi|192305754|gb|FG995710.1|FG995710
EST:     ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG                         ACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
genomic: ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGGgtaaaatttc ... gaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
EST: gi|192294844|gb|FG987533.1|FG987533
EST:     ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG                         ACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC
genomic: ATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGGgtaaaatttc ... gaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaaagttatgcatcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT
                                 tattttcttattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataacccttattcttatttgtttcataatcgtttgatatttaattagaaagttatgcatcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatg