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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctagttttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG

Basic information

species Glycine max
transcript GLYMA15G13580.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g40370.1 (Oryza sativa), 3'ss of exon 4
----ttctagttttgtttaacacttatgat-gtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG----
         |   ||||  |  |  |  || || |||       | |||||||| | |  | ||  || ||   |  |     |  |||  | |    ||| |||||||||||||||||||||||||| ||||| || || |||| |||| ||||  ||||||||||||| ||  |    
aaaaagaacggaatgttgcatgcggaaaatagtgtctataaccatatttgttgaagctgtacttctga-cagagtgga----tttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 6
----ttctagttttgtttaacacttatgat-gtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG-----------------------------
         |   ||||  |  |  || || || ||| |     | ||||||||  ||  | ||   |   |||    |  ||   |||  | |    |||  ||||||||||||||||||||||||| ||||| || || |||| |||| ||||  |||||||||||| | |||                              
aaaaagaatggaatgttgcatgcggataatagtgtctagaaccatatttgttgaaattgtacttctcac--tgagtggatttc---cattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 17
--ttctagt-tttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG
   ||||||  | || |||||  | || ||| || ||   |        |     |  |||| ||||  |     ||  ||||   |  | | |  ||| ||||||||||| |||||||||||||| || ||||| || |||||||| ||||| ||||| ||||| || || ||
gaatctagtactagtataacaagtgtgttgtgtcctgatgtccagcaagtataaatgtattttcgatagt--ctgaatttctgtgctcctgttt-cctttcagGATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAG

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 15
-----ttctagttttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG-----------------------------
         | | |||  |     | ||   || ||| |     | |||||||| | |  | ||  ||   |||    |  ||   |||  | |    ||| |||||||||||||||||||||||||| ||||| || || ||||||||  ||||  |||||||||| || ||  |                             
aaagaacagaatgttgcatgcggataatatagtgtctagaaccatatttgttgaagctgtacttttga--gtgagtggatttc---cattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGGTAATTTGTGATCTTAAAACATACTTTGG

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g40340.1 (Oryza sativa), 3'ss of exon 15
-----ttctagttttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG
         | | |||  |     | ||   || ||| |     | |||||||| | |  | ||  ||   |||    |  ||   |||  | |    ||| |||||||||||||||||||||||||| ||||| || || ||||||||  ||||  |||||||||| || ||  |
aaagaacagaatgttgcatgcggataatatagtgtctagaaccatatttgttgaagctgtacttttga--gtgagtggatttc---cattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 8
---ttctagttttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG
   |   |  |    | || |   |  || |   ||  | |    | |   | | ||||  | | ||     |  |   | |  | | ||   | |||| |||||||| ||||||||||||||||| || || ||||| ||||||||||||||  ||||||||||||| || ||
ggatatgaagtgcaataaatatgaactatattgtttttgctcaagtagaaaaaggttgaacttctatatcagtggactgtttttcttcat---tctctttcagGATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G000039_T01 (Zea mays), 3'ss of exon 18
-----ttct--agttttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttac-gat-catgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG
     |||   |||  ||||||  | | ||  | |    | | |||    ||   || ||  || | | |||   ||||      |      || ||| | |    |||||||| ||||||||||||||||||||||| ||||| || || ||  | ||  | ||||| ||||| |||||
gtatattcagaagtactgtttag-attcattgtatcatcttgcattgaactgaacagattgtatctcctgatgtttgatgtttttttctggttattatatctgccacagGATGTATATTTTGATGATGAATCTGCAGAGGTTGTAATCTCCTCCCTTCGCCTTGGAGACGACCAAGAAAG

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G096107_T01 (Zea mays), 3'ss of exon 18
-----ttctagttttgt-ttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG
     |||   |||  | || | | | ||  | |   || | |||    ||   || || | | |  |||  |  |      ||||   || ||| | |   ||||||||| ||||||||||||||||||||||| || || || || ||  | ||  | ||||| ||||| |||||
gtatattcagatttactgtttatattcattgtatcatttcgaattgaactgaacagatt-ggtgtttgatgtttttc-----tctggt-tattatatctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGCCTTGGAGACGACCAAGAAAG

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
ttctagttttgtttaacacttatga-tgtatct-tgggatttttttgttgaggtttgatt--tacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG
  || | |  |     | | | ||  ||| | | |  |       | | || | || | |  || | |    || ||| | ||   || |  | ||| |||||||||||||| ||||||||||||||||||||||| || ||||| || |||||  | ||||||||||| || ||
-actcgctcagc--ggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaa-acctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG

upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
ttctagttttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgta---tcttg-cagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG
   | |||| ||  |   ||  | |||| || |  |   ||  | ||||      |   |  ||  ||  |||  |  |  | |  |||| |   ||||| ||||||||||| |||||||||||||| || |||||||| ||||||||| |||| ||||||||||| || || ||
-cattgtttagtcgactgctc-tcatgt-tcataagccattgct-ttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG

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|208284424|gb|GE083740.1|GE083740
EST:     GTTCATGGCTCTCTTGAACGAGATGATGAG                         GATGTCTATTTTGATGATGAATCTGCA
genomic: GTTCATGGCTCTCTTGAACGAGATGATGAGgtatgatgtt ... tatcttgcagGATGTCTATTTTGATGATGAATCTGCA
EST: gi|9565802|gb|BE475311.1|BE475311
EST:     GTTCATGGCTCTCTTGAACGAGATGATGAG                         GATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGG
genomic: GTTCATGGCTCTCTTGAACGAGATGATGAGgtatgatgtt ... tatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG
                              atctgac  putative branch site (score: 3)
                                     ataatatgtatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctagttttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctga