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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

Basic information

species Glycine max
transcript GLYMA18G26190.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 4
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtc--tctgctttcctttgtctacaaactaattttc-tttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
      |   | |||||  |||   | ||||||     | | || ||  | |||||| ||  |        ||||| |   | ||   || |||     ||||| || || ||||||||||||||||| |||||| |||| || || || || ||||| || ||||| ||||||||||||| ||| ||||||||| | |||||
-----gtagatgtttaa-gatgct-tacatttgaatggttatgtttcattttgctttgctg-gcaggtgttctaatgtgaatgttccatttttatactgacagGTACCCCCTGCTTCCGTGGATATGGCAGGCGTGATGGTGAGCGCAGAAGGAAGTCAGTCCGTGGTTGCATTGTCAGCCAAGATCTCTCTGTTATCAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 4
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatt-tgttacttg---aacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
                         |  |   | | |||      | |   |||||   | |  |    ||   | |     |||| |||||||||     |||| || |||||||||||||| ||||| |||||| |||| || || ||||| |||||||| ||||| ||||| |||||||  ||||| |||||| | |||||
------------------------gtaaaaaggctctatttctattattgactttcggatattcatgcccttgctctgaccatattatgttacttgtatggcagGCACACCTTGCTTCCGTGGGTATGGCAGGCGTGATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTCAGCCAGGACCTATCTGTTATTAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G054136_T06 (Zea mays), 3'ss of exon 3
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgt-ctct----gctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
     |    |   ||    | |   | | ||  | | ||  |||| ||||     |  || |||      |  || || |     ||   | | | ||    ||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| |||||||| ||||| ||||| || |||| |||||| |||||| | |||||
----ttctgctccataggggtatagag-acttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
            | ||   |  || |   |    ||||     | ||    |  || |||      |  || || |     ||   | | | ||    ||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| |||||||| ||||| ||||| || |||| |||||| |||||| | |||||
-----------gtatagagacttcctatgtccagtgtac----tctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
            | ||   |  || |   |    ||||     | ||    |  || |||      |  || || |     ||   | | | ||    ||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| |||||||| ||||| ||||| || |||| |||||| |||||| | |||||
-----------gtatagagacttcctatttacagtgtac----tctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G851698_T01 (Zea mays), 3'ss of exon 4
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT-----------------------------------------------------------------------
                                                                        || |     ||   | | | |||   ||| ||||| |||||||| || ||||| ||||||||||| || || ||||| |||||||| ||||| || ||||| |||| |||||| |||||| | |||||                                                                       
-----------------------------------------------------------------------tatctgaacatttgatatgaattgtgtaggcactccctgcttccgcggttatggcaggcgtaatggtgagcgcaggaggaagtctgtccgtggttgtattGTGAGCCAAGACCTATCTGTTATCAACTTGGTAATTGTTAAGAAGGGTGAGAACGATCTGCCTGGTTTAACTGACACTGAGAAGCCAAGGATGAGGGGTC

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 4
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgcttt-cctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
         | | |  |   | || | |||| ||  | |||     | ||  ||| ||| ||  |   | || |    | ||| || ||  | |||   ||| ||||| |||||||| || ||||| ||||||||||| || || ||||| |||||||| ||||| || ||||| |||| |||||| |||||| | |||||
--------gtatatagactgtatc-tccatt-gtactctcaacaccccctcttttacctgtggttcttatctgaa---catttgatatg--aattgtgtagGCACTCCCTGCTTCCGCGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGTATTGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgt-ctct----gctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
     |  | |   ||    | |   | | ||  | | ||  |||| ||||     |  || |||      |  || || |     ||   | | | ||    ||| ||||| ||||||||||| ||||| ||||||||||  || || ||||| || ||||| ||||| ||||| || |||| |||||| |||||| | |||||
----ctctactccataggggtatagag-acttcctatgtccagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 4
---------ctttattcattttttaataatgtcatgcatttgttgtatcagg---tgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
         | | || | |||| | | | | |      | |  || ||  |    ||| | ||  |   |||  ||  | | |||  || |||     |  |   ||||||||||||||||||||| | ||| |||||||| | | ||| ||  | || ||||||||||||||||| |||||||| ||||| || ||||||||| ||||| |
gtaactaaacataataccttttcttacacttttgcatctataatggatttgtatttgtgtgtgtgtgtgttttgctgtagattaacattgttt---cgtaatgggtgaacagGAACTCCTTGCTTCAGAGGACATGGAAGGAGAACTGGTGAGAGGAGAAGAAAGTCTGTTCGTGGTTGCATTGTGAGCCCTGATCTCTCTGTTCTGAACCT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------------------------ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
                                                                                          | |||   | |||  | |||  |  ||||||   ||   |  | |   |  | |||  |    ||||||||     ||    || || |||||||||| || ||||||||||||||||||||||| ||||||||||| || ||||| ||| |||||||||| |||||||| ||||  |||||||| |||||||||||
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgat---gaaactaatacgaattggcatt-ttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 4
---------------ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
               || |  | ||  || || | ||      |    |    |||  | | | |||     |  |||||  |  |   || |  |||||   ||| |||| |||| || || |||||||||||||||||||| ||||||||||| || ||||| ||| |||||||||||||||||||||||| |||||||||||||||||||||
gtgagtaaactgggactgttctaatccttaaaaactgatcacaacccttaagttcatatttttatgcaagt-tgggtctatgagatttattacactttatgc-ttatttgagcagGTACCCCATGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGGTGCATTGTCAGCCAAGACCTCTCTGTTTTGAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgcttt-cctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
                                                            |   |||        ||    ||||  ||  | | | || || |   ||| ||  | | |   |   |  ||   | || |  |||  | ||| | ||||||| |||||||| || |||||||| ||||||||||||||  | ||||| ||| |||| |||||||||||||||||||  ||||| |||||| |||||||
gtgggtttttggtggtatattagtgttggtgcactgaccaccattccttcaagtttaagatggatcacggccagttagaagcatgttttgctaggaccatgttttgttgccttgtcatagatgatggatgaaaactgttctagttt--tgcttaagcagGAACCCCTTGCTTTCGAGGATATGGTAGGCGTAATGGAGAGAGGAGGAGGAAGGCTGTACGTGGGTGCATTGTCAGCCAGGACCTTTCTGTTCTGAACTT

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_322V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctt-tgtctacaaactaattttct-----ttttatttgttacttg---aacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
                                           ||  |   | |   || |   |  | || | |  |   ||| |  |   ||   | | | |  ||| || |||||||  |     || || ||| |  ||      ||||     |||||||||| ||||| || ||||| || || || |||||| ||||||| ||| | ||||||||||| || || |||||||| ||  ||||| |
gtacaatattgattaattggaacctcatggtctgaagttgtgcctgcaaggaatccgtactg--gatacgcgtctcgt-cgtcatgcattcttgtactgcatgtcactaaaatctaatttcttaacgattgtacttgatgttttctcggcagGTGTCTCTTGCTTCCGAGGATACGGGAGGCGCAACGGCGAGCGTAGGCGAAAGTCCGTTAGAGGGTGCATTGTGAGTCCCGACCTCTCAGTGCTGAACCT

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|209699698|gb|BW652083.1|BW652083
EST:     GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGG                         GAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
genomic: GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGGgtatgatgta ... acttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
EST: gi|6482119|gb|AW201390.1|AW201390
EST:     GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGG                         GAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
genomic: GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGGgtatgatgta ... acttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
EST: gi|6667651|gb|AW279102.1|AW279102
EST:     GCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGG                         GAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
genomic: GCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGGgtatgatgta ... acttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
EST: gi|19053288|gb|BM731955.1|BM731955
EST:     GTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGG                         GAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
genomic: GTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGGgtatgatgta ... acttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
EST: gi|308097910|gb|HO761081.1|HO761081
EST:     GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGG                         GAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
genomic: GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGGgtatgatgta ... acttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
EST: gi|192296729|gb|FG991297.1|FG991297
EST:     GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGG                         GAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
genomic: GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGGgtatgatgta ... acttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
EST: gi|298187174|gb|HO034323.1|HO034323
EST:     GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGG                         GAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA
genomic: GAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGGgtatgatgta ... acttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
                      aactaat  putative branch site (score: 2)
                            ttttctttttatttgt  CT-rich tract
                  tacaaactaattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

- - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - -tgttgta