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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG

Basic information

species Glycine max
transcript GLYMA19G35980.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35980.4 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g02880.1 (Oryza sativa), 3'ss of exon 3
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG
                                                             | ||   |  | |     ||  | |||   |        | | |||||  |  | |  | |    |     | |||   |   | |   |||| |        ||||| || |||||||| || |||||||| || ||||| || ||||| |||||  |||||||||||||||| || ||| |||| || ||||| ||||||
------------------------------------------------------------gtatgtgaattattcttccctcatttttttctctcttttctaaattgtaccttttagt-tcacaagtccaacatttttcggatgtctcttttacca------aacagGAGTTCAGTGATCCCCGTGATGCTGAGGAAGCAAGGTACAACCTTGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGG

upper sequence: GLYMA19G35980.4 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 3
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG----
                        ||| |    | |||  |   |||   ||| ||  |||  | ||      |   ||  |||  ||  |  |  | |||  |||  | ||      |||| | || | ||    |   | | | |   |||| |        ||||| || |||||||| || ||||||||||| ||  | |||||||| |||||  |||||||||||||||| || ||| |||| || ||||| |||||     
-----------------------gtatgtgaatacttccctcatttt---tttattgcgtaacttctc-----tctttttaagttctta-tgaggtgtattttgtt-cacat------atgagtcctatatt----ttgcgacatctattttacca------aacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGAGTAA

upper sequence: GLYMA19G35980.4 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG
                        ||| |    | |||  |   |||   ||| ||  |||  | ||      |   ||  |||  ||  |  |  | |||  |||  | ||      |||| | || | ||    |   | | | |   |||| |        ||||| || |||||||| || ||||||||||| ||  | |||||||| |||||  |||||||||||||||| || ||| |||| || ||||| ||||| 
-----------------------gtatgtgaatacttccctcatttt---tttattgcgtaacttctc-----tctttttaagttctta-tgaggtgtattttgtt-cacat------atgagtcctatatt----ttgcgacatctattttacca------aacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA

upper sequence: GLYMA19G35980.4 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G175419_T01 (Zea mays), 3'ss of exon 3
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG
                     || | | || |    |    | | |||||||    |  | ||  ||  | | |||   || |    |  | | || |||| |     | ||  ||   | |||   |  ||  ||  |  |    || ||||  | |      ||||| || ||||| || || |||||||||||||||   || ||||| |||||  |||| || |||||||| || |||||||| |||||||| ||||||
---------------------gtatgtgtactttactgccctcagttcaattctgcaactgttacctatataatggtggcttgctcatattat-agaaattgaaaaaaacatt-tgttttaattgtggcattctttattgtgacccttggtta--attgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG

upper sequence: GLYMA19G35980.4 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatg---atttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG
||| ||    ||| ||| ||  ||||||| ||   | |||||  | ||  || ||||||  | ||    |   |   |     |||||   |  || | |    || |||||| ||  |     || |  |  |  | || || | |  | |  |  |  || |   ||||| || |||||||| ||||||||||||||||||||||||||| |  |||| || ||| ||||||||||||| || |||||||||||||| ||||||
gtatgtatcaaccatttgttcatctatttctt---tcctttt--tctcccttgcttatggttatg---gagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG

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|213619830|gb|DB969494.1|DB969494
EST:     AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
genomic: AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTTgtaagttgtc ... ttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
EST: gi|208106711|gb|GD906528.1|GD906528
EST:     AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
genomic: AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTTgtaagttgtc ... ttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
EST: gi|15286621|gb|BI470512.1|BI470512
EST:     AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
genomic: AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTTgtaagttgtc ... ttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
EST: gi|209715287|gb|BW654174.1|BW654174
EST:     AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
genomic: AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTTgtaagttgtc ... ttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
EST: gi|213599416|gb|DB970364.1|DB970364
EST:     AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
genomic: AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTTgtaagttgtc ... ttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
EST: gi|17023537|gb|BM094571.1|BM094571
EST:     AGAGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
genomic: AGAGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTTgtaagttgtc ... ttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
EST: gi|298181985|gb|HO026160.1|HO026160
EST:     AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT
genomic: AGTTCGAGGTGTGGATATGAAGAATGATTTCGCTTTTGTTgtaagttgtc ... ttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG
                                            ctttt  CT-rich tract
     aatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG