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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgagaatcgaaaccagccaaatgaaacaacaaaatataaccaaatttttagcatgtgcgtgtacgacacatgtatattaattcctcttctcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTTTCCCCATTTGGGAAG

Basic information

species Glycine max
transcript GLYMA07G09180.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G09180.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g17680.1 (Oryza sativa), 3'ss of exon 3
--atgagaatcgaaaccagccaaatgaaacaacaaaatataaccaaatttttagcatgtg-cgtgtacgacacatgtatattaattcctcttctcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTTTCCCCATTTGGGAAG
  ||| |||||       |  ||  || |     | ||        |  |  |     || |||     |    | | | ||  ||   ||| |    ||||||| |||||||| ||||||||||| ||||| || |||||||| ||||| || |||||||||||||||
gcatg-gaatcattgtaggttaagagataaggtgagatggggttggagatggaaatgatggcgttcttaattagtatgttttgcttgtgcttttt--cttcagGTGAGGAAGGAGAAGCTAGGTGATAGAATAACTGCCCTTCACCAGCTTGTCTCCCCATTTGGGAAG

upper sequence: GLYMA07G09180.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 3
atgagaatcgaaaccagccaaatgaaacaacaaaatataaccaaatttttagcatgtgcgtgt-acgacacatgtatattaattcctctt-ctcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTTTCCCCATTTGGGAAG
|  ||||   | | |   ||  ||  | ||  |   | ||     |||    || || |   | |    ||   ||| || ||   | |   |     |||||| |||||||||||| ||||||| |||||||| |||||||| ||||| || |||||||||||||||
agaagaaagtagatcgttcacttggtagaa--agccaaaatttcttttcacccacgtcctcatcatccaactcttatttttatgtatttaatttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
















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|120493651|gb|EH221818.1|EH221818
EST:     TCAAGAAAGCTAGGGTTCAACCCTCTGCTACAACGCAGACTACGTTCAAG                         GTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTT
genomic: TCAAGAAAGCTAGGGTTCAACCCTCTGCTACAACGCAGACTACGTTCAAGgtaaaatgca ... tcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTT
EST: gi|120493768|gb|EH221935.1|EH221935
EST:     TCAAGAAAGCTAGGGTTCAACCCTCTGCTACAACGCAGACTACGTTCAAG                         GGTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGGCCTTCATCAGCTCGGT
genomic: TCAAGAAAGCTAGGGTTCAACCCTCTGCTACAACGCAGACTACGTTCAAGgtaaaatgca ... tcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTT
EST: gi|19348059|gb|BM892591.1|BM892591
EST:     TCAAGAAAGCTAGGGTTCAACCCTCTGCTACAACGCAGACTACGTTCAAG                         GTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTT
genomic: TCAAGAAAGCTAGGGTTCAACCCTCTGCTACAACGCAGACTACGTTCAAGgtaaaatgca ... tcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTT
EST: gi|208239088|gb|GE037166.1|GE037166
EST:     GCTAGGGTTCAACCCTCTGCTACAACGCAGACTACATTCAAG                         GTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTT
genomic: GCTAGGGTTCAACCCTCTGCTACAACGCAGACTACGTTCAAGgtaaaatgca ... tcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttagcatgtgcgtgtacgacacatgtatattaattcctcttctcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTTTCCCCATTTGGGAAG
                              tattaat  putative branch site (score: 2)
                                    ttcctcttctcaattt  CT-rich tract
                       acatgtatattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgagaatcgaaaccagccaaatgaaacaacaaaatataaccaaatttttagcatgtgcgtgtacgacacatgtatattaattcctcttctcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTTTCCCCATTTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC