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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccgaaacagatcatgtttgtcacatctatcaacataaagttactgttttaatccttcttaactgttacttaaaacttggttgtcaaatttgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG

Basic information

species Glycine max
transcript GLYMA03G27380.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 3
gccgaaacagatcatgtttgtcacatctatcaacataaagttactgttttaa--tccttcttaactgttacttaaaacttggttgtcaaatttgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG
|      | || |   |  ||    |  ||  ||  | ||||     |  |   |  | ||   ||  |  |  ||   |  ||||      |    ||||||| ||||| || ||||| || |||||||||||||||||  | ||||| ||||| ||||| ||  |||| |||||||| ||||||||||| || || |||
gtaatctccgagctattccgttgtttgcatggaccaacagttcacactgaagattgttactgtgctcctcttctaacagtttttgtgtgtgatcctttgcagGTGTATGTGACCATGTACCTAAATGATTGCCAACGTACTACATTCTATGAAGGGATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATAATTGAG

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G081462_T01 (Zea mays), 3'ss of exon 3
gccgaaacagatcatgtttgtcacatctatcaacataaagttactgttttaatccttcttaactgttacttaaaacttggttgtcaaatt-tgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG
   | ||          || ||   |  ||  |||| |  |  ||       |   |     |   | || | | ||  |||   | ||    |  ||||||| ||||| || ||||| || ||||| |||||||| || || ||||| || || ||||| ||  |||| |||||||| ||||||||||| || ||||||
---gtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAG

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 3
gccgaaacagatcatgtttgtcacatctatcaacataaagttactgttttaatccttcttaactgttacttaaaacttggttgtcaaatt-tgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG-
   | ||          || ||   |  ||  |||| |  |  ||       |   |     |   | || | | ||  |||   | ||    |  ||||||| ||||| || ||||| || ||||| |||||||| || || ||||| || || ||||| ||  |||| |||||||| ||||||||||| || |||||| 
---gtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 4
gccgaaacagatcatgtttgtcacatctatcaacataaagttactgttttaatccttcttaactgttacttaaaacttggttgtcaaatttgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG
                   || |  |  |  ||  |    ||| | | | |||   ||||     ||     ||     ||      ||| |   | ||||||||||| |||||||| |||||||| |||||| | ||   ||||||||| || || ||  | |||||||| || || || ||||||||||| ||||||
-------------------gtaat-taaactaaactctctttagt-tctcaatgtgtcttgcacattggcctaa--ccagtaagaggattggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------gccgaaacagatcatgtttgtcacatctatcaacataaagttactgtttt---aatccttcttaactgttacttaaaacttggt----tgtcaaatttgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG
                                              ||  | |         ||| | ||     |     ||||  |   | ||    |   | |||    |    ||       |  |    |  |||||||||| ||||||||||||| |||||||| |||||||||||||| ||||| | |||||| ||||| ||||| || |||||||||||||||||||||||||| || || |||
gtaattatagtataataagtttctacattcaattgtatactagattgcaaatattatcttaattttttaccctagtgtgtttaaatctttggcttctcgagaacctctgggattcctctggtcctcttatgacttcccaaatttgtcttgcagGTTTATGTAACAATGTACCTCAATGATTGCCAGCGTACGGATTTCTATGAAGGAATTGGGCTCAACACAAAAGAATTTGACATGCATGTGATCATAGAG

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|105633520|gb|DW246883.1|DW246883
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTCACAATGTATCTCAATGATTGCCAACGT
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaactattc ... tgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGT
EST: gi|209726223|gb|BW659575.1|BW659575
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaactattc ... tgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAA
EST: gi|213602652|gb|DB978095.1|DB978095
EST:     TTCTGTCTATCG                         GTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
genomic: TTCTGTCTATCGgtaactattc ... tgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAA
EST: gi|151399052|gb|EV268923.1|EV268923
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAA
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaactattc ... tgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttaatccttcttaactgttacttaaaacttggttgtcaaatttgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG
           tcttaac  putative branch site (score: 2)
                                           tttgtcct  putative PPT
                    ttacttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccgaaacagatcatgtttgtcacatctatcaacataaagttactgttttaatccttcttaactgttacttaaaacttggttgtcaaatttgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- -gaaacaga
- - - - - - - tgtttgt
- - - - - - - - - - - - - - atcaaca
- - - - - - - - - - - - - - - - - - - -gttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttac