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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatgtttttaatcatctacttcaacccttttcattagcattatcattatcatttttgaaagagaatgcacacttataattcttaatctgttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG

Basic information

species Glycine max
transcript GLYMA15G14550.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
tctatgtttttaatcatctacttcaacccttttcattagcattatcattatcatttttgaaagagaatgcacacttataattcttaatctgttgttaaa--gGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
                |    || ||  |  |  |||  | ||    |  ||  | | ||| |   |   ||    ||| |  ||  |||||    |||  ||| || ||||||||||||| |||||| ||||| || ||||||||||| || |||||||||||||||||| | ||||||||||| |||
---------------gtaagtttgaaagcaat--att--ccttgatctggtccatctggaatgtatacaaactgacatactgttttctctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG

upper sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 5
tctatgtttttaatcatctacttcaacccttttcattagcattatcattatcatttttgaaagagaatgcacacttataattcttaatctgttgttaa-agGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
          |||  ||  ||   | |    ||   |    |  | | |||  |||  | |||  | ||   || |||  ||  |  | || |   |  |||| || ||||||||||||| |||||| |||||||| ||||| ||||| ||||||||||||||||| ||| | |||||||||||||||
---------gtaagaataaacaaaagcaacattttctcatgtgctgaatatgctttaggtaagcaactg---acatatggtttct--tttgctcaaattagGCTGATGAGATGGCTCAGATATTCAGGCAGAGAATAGCTCAGGCAGAGGCTATGGCTCGTGCTGACATGTTGAGATTCCAGCCAGAG

upper sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
tctatgtttttaatcatctacttcaacccttttcattagcattatcattatcatttttgaaagagaatgcacacttataattcttaatctgttgt-taaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
                   |||  |   |  ||||  |  | | ||  |||  | ||| |         ||  | | |  | |||  |||| ||| | ||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||| | ||||| || |||
----------------gtaactctatttccattcaaaaaaactttccctattttcttttatgt----ctcaatcatttgctactt--tctgctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG

upper sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 3'ss of exon 5
tctatgtttttaatcatctacttcaacccttttcattagcattatcattat-catttttgaaa----gagaatgcacact-tataattcttaatc-tgttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
       || |  |  |  || |  |  |    |||  |  ||     | | | | |||||||    | || |  ||| |   |   |||||| | |||| | | |||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| || || ||||| |||||||| || |||
-------ttctgttacttcacctataaaccacacatgtgtgttgctcctctacctatttgaaatccagtgatttaacaatacttggctcttaaccctgttctaacagGCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAG

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|18038939|gb|BM307233.1|BM307233
EST:     AACCCACACCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAG                         GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
genomic: AACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAGgtataataca ... gttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
EST: gi|18038907|gb|BM307201.1|BM307201
EST:     AACCCACACCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAG                         GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
genomic: AACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAGgtataataca ... gttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
EST: gi|18732823|gb|BM527270.1|BM527270
EST:     AACCCACACCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAG                         GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
genomic: AACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAGgtataataca ... gttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
EST: gi|7234320|gb|AW569659.1|AW569659
EST:     AACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAG                         GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
genomic: AACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAGgtataataca ... gttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
EST: gi|15001176|gb|BI321990.1|BI321990
EST:     ACGCCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAG                         GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT
genomic: ACGCCTGGTGACATGATTCGCAATCCAAAGCTTGTCTTTGAGAAGgtataataca ... gttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatcatttttgaaagagaatgcacacttataattcttaatctgttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG
                                    tcttaat  putative branch site (score: 3)
                           acttataattcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctatgtttttaatcatctacttcaacccttttcattagcattatcattatcatttttgaaagagaatgcacacttataattcttaatctgttgttaaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - tcaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca