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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattcagaaataggtgaaaaatggtgacttgttagtgcttcaattacatcgaattgtgtttcttcgtttcttttccttaattggtttgccaaggtaactatgttttcttccgcaatgcag

Basic information

species Glycine max
transcript GLYMA19G35710.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 3
ATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaag-cattcagaaataggtgaaaaatggtgacttgttag-tgct--tcaattacatcgaattgtgtttcttcgtttcttttccttaattggtttgcca-aggtaactatgttttcttccgcaatgcag-----------------------------------------------
    | |   |          ||  | || |||||||||||  | ||||||||| ||| |||||||||||| |||||||||||||||||||||||||| |||||   | ||  || |   |     |   |    |  ||  ||||  ||||  || ||   |||   |  |||||| ||  |  | | ||  || |  | | || ||  |      |||    ||                                                   
TCCACCCGCGAGGGGAAGGCACCAGCTCTCAATGAGAGGATACTCTCATCCATGTCCAAGAGATCTGTTGCAGCACACCCATGGCATGACCTTGAGATTGgtaaaatactcgtaactctattctctactctactctactaactgctgctcaaccacctcactttggagtatttcgttactagtagtgatttccttgggtacacgttacccttcagatttctattatatttcttaggttcaaaaattcatcattttccctcctttgctttgcttgcag

upper sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 5'ss of exon 2
ATTTCTCATCATTCCTCACA--CCCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattcagaaataggtgaaaaatggtgacttgttagtgcttcaattacatcg-aattgtgtttcttcgtttcttttccttaattggtttgccaaggtaactatgttttcttccgcaatgcag
    |||| |   | |||    |||| | || ||||| |||||  | ||||| ||| || |||||||| |||| ||||| ||||||||||| |||||||| ||||           ||   ||| |||   | | || |   |  |||  | | | |  | || |   |    |  |  || |   |                                         
--GGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgacatttcatct-tgacaaaccatcaattttctatatttctctcataacttacttataggttcctgacttcttcctgcag----------------------------------------

upper sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
ATTTCTCATCATTCCTCACAC-CCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaa-gcattcagaaataggtgaaaaatggtgacttgttagtgcttcaattacatcgaattgtgtttcttcgtttcttttccttaattggtttgccaaggtaactatgttttcttccgcaatgcag
      || | | |   |    ||| || | || || |||||  | ||||||||| ||||||| ||||||||||||||||| |||||||| || ||||||||||  | |  |         ||| ||||||| |   |||  | ||    |     | |   | | ||       ||||    | |    |                                    
-ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacgctctagcttgacaaatggtcagccgttgat-ctctgctatttgcaaccagagcttaagttcatcttggattcatgcag------------------------------------

upper sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 2
ATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattcagaaataggtgaaaaatggtgacttgttagtgcttcaattacatcgaattgtgtttcttcgtttcttttccttaattggtttgccaaggtaactatgttttcttccgcaatgcag
 ||    | |||   ||||  ||| | ||||||||||||||  |||| |||||||     ||||| || |||||||||||||||||||| || |||||||||||||        ||| || ||       |  || ||  |  ||   ||   || ||     |||| | |||| ||     ||| |  | | ||    |  ||  |  ||| |  |   | |||
GTTGAGAAACATGTTTCACTTCCTACTCTTAATGAGAGGATACTTTCGTCCATGAGTCACAGATCAGTAGCTGCACACCCATGGCATGATCTCGAGATAGgtaagct-------atacgtaaa-------ggtttctttttcttttttttggctctaagatcatttcattgttttttagtaataactcttataccttttttgcttcgcattcctttgtt-tacag

upper sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 2
ATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattcagaaataggtgaaaaatg-gtgacttgttagtgcttcaattacatcgaattgtgtttcttcgtttcttttccttaattggtttgccaaggtaactatgttttcttccgcaatgcag
|  ||||||||   ||||||||| || |||||||| |||||| |||||||||||||| ||||  |||||||||||||||| |||||||| |||||||||||||   | |           | |   || || | || ||| ||  ||  ||  | | | | |  |||  |  |  | |||  |   |   |                                   
AACTCTCATCAACACTCACACCCACCTCTTAATGAAAGGATTCTTTCATCCATGACCCGGAGGGCTGTTGCTGCACACCCCTGGCATGATCTTGAGATAGgtacctacttttgttgtaacgcatgttgagttaattcttaatgtctccttttta-ctagtggccttttattatgacattttttatttcaatgcag-------------------------------

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|192301012|gb|FG990112.1|FG990112
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|10844730|gb|BF067948.1|BF067948
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|254335061|gb|GR844846.1|GR844846
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|9901982|gb|BE610950.1|BE610950
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|193534902|gb|FK489066.1|FK489066
EST:     CATGACCAGGAGATCTGTTGTTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|193665609|gb|FK609230.1|FK609230
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|22523592|gb|BU082403.1|BU082403
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|193635563|gb|FK582088.1|FK582088
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|193314904|gb|FK281404.1|FK281404
EST:     CATGACCAGGAAATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|193576426|gb|FK530793.1|FK530793
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCTAATTTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTC-AATT-GT
EST: gi|254335060|gb|GR844845.1|GR844845
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|208305097|gb|GE102798.1|GE102798
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTG
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTG
EST: gi|151398751|gb|EV268622.1|EV268622
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|298189455|gb|HO037858.1|HO037858
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|208126482|gb|GD924788.1|GD924788
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGTGTGATTG
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGTGTGATTG
EST: gi|8669991|gb|BE191098.1|BE191098
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|17964359|gb|BM271095.1|BM271095
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|120533838|gb|EH261971.1|EH261971
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|298182727|gb|HO031462.1|HO031462
EST:     CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTATCTTCAATTGT
genomic: CATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAATTATCTTCAATTGT
EST: gi|207833133|gb|GD801810.1|GD801810
EST:     CACACCCATGGCATGACCTTGAGATAG                         GACCTGGTGCTCCAATTTATTCTTTCAATTGT
genomic: CACACCCATGGCATGACCTTGAGATAGgtaagcattc ... cgcaatgcagGACCTGGTGCTCCAA-TTA-TC-TTCAATTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCTCATCATTCCTCACACCCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattcagaaataggtgaaaaatggtgacttgttagtgcttcaattacatcgaattgtgtttcttcgtttcttttccttaattggtttgccaaggtaactatgttttcttccgcaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC