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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagtaccaatttgataacggttgttctgttaacaattcccccattcttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG

Basic information

species Glycine max
transcript GLYMA09G06640.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagta--ccaatttgataacggttgttctgttaac--aattcccccattcttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
                       | |   || | | |   |  |    |  |  || | ||      |  |    |||  | |         | ||||| ||||    ||||  |  ||      |    ||| ||    ||  |||| ||   | |      | |   | ||  |  || |        | | | |    ||||||||||||  | ||||| |||||||  ||||| ||||| ||  | |||||||| || |||||||| ||||||||||| |||||||| ||||| ||
----------------------gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatac---------atgaaaattgttc---tgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG

upper sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagtaccaatttgataacggttgttctgttaa-caattcccccattcttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
                                                                                                          | |||||| ||||  | |      |||  ||       ||||| |  |||| |  ||| ||| ||      |  |  || || ||||       ||||||||||  |||| |||||||| |  || || |||||  |||||||||||||  |||||||||| ||||| ||||| |||||||| ||||| ||
---------------------------------------------------------------------------------------------------------gtttgtctt-taaa-gttgtctccaggtgttaggggga-gataatg-ctgttgtactaagcaaatct---gattatgctggattttca-------gTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG

upper sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagtaccaatttgataacggttgttctgttaacaattcccccattcttcttgc---atcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
                                                                                                    ||| |   |   || |    |||  |  |  | | | |  |||      |   | ||   ||   |     |   || ||||  |   |  ||   ||  |||||| |||||  ||||||||||||| |  ||||| ||||| ||||||||||| ||  |||| ||||| |||||||| || |||||||| ||||| ||
-------------------------------------------------------------------------------------------------gtttgtcttgttaattttttttaataatatctcagaactgcttattcctctgcacat-tttgatttgtatgcttctttttgttctaacgaaaaattggcctttcagTCACACAGCAGCTATTGCAGCTGGGAACAATGGTATTCCAGTGAGGATGCACGGTTATGAGTTTGGAAAAGCAAGCGGGATGGCTCCTCGTGCAAG

upper sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 4
gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagtaccaatttgataacggttgttctgttaacaattcccccattcttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
                                                                                     |  |||     |   | |||  || | || |   |||    | |  ||  ||     |||     ||||  | ||||              | |  | | |           |||||| |||||  |||||||||||||||  ||||||||||| ||||| ||||||||  |||||||||||||||||||||| |||||||||||||||||
-------------------------------------------------------------------------------------atgatagtttgattttcttttaatattttgttcccattt--actctgttttatttgattgggtctggttcatttgttg-------------tttcttgggaatactggacaacagTCACACAGCAGCTATTGCAGCTGGAAATAATGGAATTCCAGTGAGAATGCATGGGTATGAATTTGGGAAAGCAAGTGGGATGGCTCCCCGTGCCAG

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|22523793|gb|BU082604.1|BU082604
EST:     AACCCTTTTATTGTTTTTGATTCACCTCTCGATGGAGATGGGCATGGGAG                         TCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCA
genomic: AACCCTTCTATTGATTTTGATTCACCTCTCGATGGAGATGGGCATGGGAGgttagaccat ... catctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacggttgttctgttaacaattcccccattcttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
             tgttaac  putative branch site (score: 2)
                      ttcccccattcttctt  putative PPT
               ttaacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagtaccaatttgataacggttgttctgttaacaattcccccattcttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA