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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcgcctggtggggaaaataactagaggaacaatgttcctatatatggtgactaatatagtgatatctgaaaaagctattattgattattataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGA

Basic information

species Glycine max
transcript GLYMA19G35710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35710.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 1
tgcgcctggtggggaaaataactagaggaacaatgttcctatata-tggtgactaatatagtgatatctgaaaaagctattattgattattataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGA-------
|  | ||  |     |  | | | ||  || |  | |  |  ||  |  | |  ||| ||||| |   |  ||  |  |  | ||  |    | | ||  | |||||    ||| |||||| |  ||||||||||| |  | |   |  ||||||||   ||||||||| || |||||||| |||||| ||||||||||||       
tatgtcttctact--atttcatttgat-aatagagctggtgaatgcttctaagaaatctagtgtttgttttaactgaaa--actgcat---gtgaatttggcttgcagTAATGGCTCCACCTATTGAGACTCCAAACAAAGCTCTTAACTCTCATCAACACTCACACCCACCTCTTAATGAAAGGATTCTTTCATCCATGACCCGGAG
















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|192301012|gb|FG990112.1|FG990112
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|10844730|gb|BF067948.1|BF067948
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|254335061|gb|GR844846.1|GR844846
EST:     ATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: ATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|9901982|gb|BE610950.1|BE610950
EST:     GTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: GTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|193466642|gb|FK432077.1|FK432077
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGTGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|208158107|gb|GD957832.1|GD957832
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|208201125|gb|GD999576.1|GD999576
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|22523592|gb|BU082403.1|BU082403
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|254335060|gb|GR844845.1|GR844845
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|208098884|gb|GD892687.1|GD892687
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|208305097|gb|GE102798.1|GE102798
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|193480869|gb|FK444308.1|FK444308
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|208294947|gb|GE089502.1|GE089502
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|151398751|gb|EV268622.1|EV268622
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|298189455|gb|HO037858.1|HO037858
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|208126482|gb|GD924788.1|GD924788
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|8669991|gb|BE191098.1|BE191098
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|17964359|gb|BM271095.1|BM271095
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|120533838|gb|EH261971.1|EH261971
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
EST: gi|298182727|gb|HO031462.1|HO031462
EST:     AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT
genomic: AAGGGCCACCGATGGTTGAAACCGAGATGGATGCAGAAACTgtaagtaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgactaatatagtgatatctgaaaaagctattattgattattataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGA
                 atatctgaaaaagcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcgcctggtggggaaaataactagaggaacaatgttcctatatatggtgactaatatagtgatatctgaaaaagctattattgattattataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAATAGTGTTTCCATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - tggtggg
- - - - - - - aaaataa
- - - - - - - - - - - - - - - caatgtt
- - - - - - - - - - - - - - - - - - - - - - -tggtgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaag