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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtatttattttacatttgccattatgatatcagattatcttaacttttggtgaggtgatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT

Basic information

species Glycine max
transcript GLYMA15G40750.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 4
-----gtgggtatttatt---ttacatttgccattatgatatcagatta-----tcttaacttttggtgaggtgatcaatttttttc--------tacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
        |  ||| |     |||    |||   | |||| |||   ||     | | | || |     |  || | | ||||||||        || |||||||||||||||||||| |||||||| |||   ||||||||||| || ||||||||||  | ||||||  | |||||||||||||| ||||| ||||||
aattatctgccattcacctacttaggactgctgctttgatgtcaagctaatgcatgtgagctctgcactatatgttgactttttttcctgttatataaagGGCTTATGGAAGTGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 4
--------------gtgggtatttattttacattt-gccattatg----atatcagattatcttaacttttggtgaggtgatcaatttttttctaca----gGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
                |  ||||  |||    |   ||  ||||     || |  | |  | || ||| || ||    |  | | |||  |  ||||    ||||||||||||| ||||| |||||||| |||   ||||||||||| || ||||||||||  | ||||||  | |||||||||||||| ||||| ||||||
gccattcacctcttaggattattgctttggtgtgaagctcttatacaatatgtgtgctcttgttcactctttgttgact--ttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 4
-------------gtgggtatttattttacatttgccattatgatatcagattatcttaacttttggtg--aggtgatcaatttttttc-------tacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
             |    |  | ||   |     |  ||||| || |    | || | | | ||  |    | ||| | | ||| ||||       |  ||||| |||||||| ||||| |||||||| ||| | ||||||||||| |||||||||||||  |  |||||| | |||||||||||||| ||||| ||||| 
tatatattatttagcatttgctgatcaaaggcgaggaattat-atgttgtgtcatgtaacccttgtgcaccatgtgttgactttgtttcattcaaattaagGGCCTATGGAAGCGGAAAAGAAGATAGCCCTCTATGTGATGTGCCTGGATTTGAAAACACTAGAATGAAACTCCTGAGACATGTTTCTTTTGTTGATTGC

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 4
-------------gtgggtatttatt-----ttacatttgccattatgatatcagattatcttaacttttggtgaggtgatca-atttttttctac---agGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
              ||   |  | |      ||| ||      | ||||  |||      | |   |     |  | |||| |  |||  || ||    ||||| |||||||| ||||| |||||||| ||| | ||||||||||| |||||||||||||  |  |||||  | |||||||||||||| ||||| ||||| 
tatttagcatttgatgatcaaatgtgaagaattatatgctgtgtcatgac-tcatgacgcccttgttcaccatctgttgattatgtttcattttaattaagGGCCTATGGAAGCGGAAAAGAAGATAGCCCTCTATGTGATGTGCCTGGATTTGAAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGC

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgggtatttattttacatttgccattatgatatcagattatcttaacttttgg--tgaggt-----gatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
||| ||  || ||  |    ||   ||||  | |     ||   |||  ||||     ||||      |   || | ||     ||||| || ||||||||||||||||| | ||| |  |||||||| || ||||||||||||  |||||||||| |  |||| ||||| ||||| || ||||| 
gtgagtccttcttacaacagtgtttttatcttctacttctactataaggtttgagtcaaggtctaacaacttatctgttgtattagGGCCTACGGAAGTGGAAAGGAAGACACTCCCAATTGTGATGTCCCCGGATTTGAAAACTCCAAGATGAAACTATTGAGGCATGTCTCATTCGTTGATTGC

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 3
----gtgggtatttattttacatttgccattatg-atatcagattatc---ttaacttttgg--------tgaggtgatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
    |  | | | || | || || |     |||  ||||| | || ||   |||||||  ||        ||   |  ||||  | ||  | |||||| ||||||||||||||||||||||||||| | ||||||||||| || ||||||||| ||| |||||| |||||  ||||||| || ||||| ||||| 
gtagggtgatgtctaatatatatatatatatatatatatctgtttttcatgttaacttcaggcttttcattgttatattcaaaatattattgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCTCTCTGTGATGTGCCTGGGTTTGAAAACTGCAGGATGAAGTTGCTACGACATGTGTCCTTTGTAGATTGC

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 4
----gtgggtatttattttacatttgccattatgatatcagattatcttaacttttggtgaggtgatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
    || | |||||| || | |  |    || | | || |  ||   |    |||   ||   |  ||||  | ||  | |||||| ||||||||||||||||||||||||||  | ||||||||||| || ||||||||| ||| |||||| |||||| ||||||| || ||||| ||||| 
gtaggttgatatttaattgatacatctattttttacattaatttcagtc--ttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC

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|209719408|gb|BW674488.1|BW674488
EST:     AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAA                         GGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
genomic: AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAAgtgggtattt ... ttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
EST: gi|209700869|gb|BW683099.1|BW683099
EST:     AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAA                         GGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
genomic: AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAAgtgggtattt ... ttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
EST: gi|192301270|gb|FG990190.1|FG990190
EST:     AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAA                         GGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
genomic: AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAAgtgggtattt ... ttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
EST: gi|192298646|gb|FG988557.1|FG988557
EST:     AAA-TATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAA                         GGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
genomic: AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAAgtgggtattt ... ttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
EST: gi|192296353|gb|FG991591.1|FG991591
EST:     AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAA                         GGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT
genomic: AAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGCCTATGTGCTACAAgtgggtattt ... ttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgatatcagattatcttaacttttggtgaggtgatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
                 tcttaac  putative branch site (score: 2)
                                          tttttttctac  putative PPT
             attatcttaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtatttattttacatttgccattatgatatcagattatcttaacttttggtgaggtgatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG