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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtcaaatcatttaaggacacttgtgtttgctttataagtgtattgctgcagtttgtcatttgacaaatattttactaatgttctgttggctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTG

Basic information

species Glycine max
transcript GLYMA03G35020.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 16
-------ctgtcaaatcatttaaggacacttgtgtttgctttataagtgtattgctgcagtttgtcatttgacaaatattttactaatgttctgttggctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTG
        | | || |  |   |  |  | | |   |||   ||| || |     |  | |   |  |   |  |  |  | ||     | ||||   ||  | |||||||||||||| || |||||| | ||||||||  | |||||||  || |||||||| ||||| ||||| ||||||||||| ||||| || |||||  | |
tctttgagttttaattgttgagaaaatgcatatacatgcagGATATGTATGA-ATTTTAATGAATACTGGCATGAGAACCTCAC----ATACTGT--ACTTATGCAGGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG

upper sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 16
ctgtcaaatcatttaaggacacttgtgtttgctttataagtgtattgctgcagtttgtcatttgacaaatattttactaatgttctgttggctgctt---cagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTG
||||  |  |   | || |||        ||   |||     | |     | ||||   | | ||  |  |||  |  ||  |        ||  |    |||||||||||||| ||||||||| | ||||| || || || |||   || |||||||| ||||| || || ||||||||||||||| | || |||||| | |
ctgttgatac---tcagtacatgcagaagtgtagtattgtgctgtaaactctgtttcagaatagaacagaattacatgaacatctcaacttctcttctggcagGATATGTATGATTTCATGGCTCTGGACAGGCCTTCAACGCCTCGCATCGATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAG

upper sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 16
ctgtcaaatcatttaaggacacttgtgtttgctttata-agtgtattgctgcagtttgtcatttgacaaatattttactaatgttctgttggctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTG
                       | |   |   ||| | |  || || |   |   |     || | |  ||| | |    |||| | | ||  | | |||||||||||||| ||||||||  ||||||||||||| || ||| |||| ||| | || ||||| ||||||||||||||||||||||| || |||||  | |
----------------------gtatagatagattagacaccgttttacattaaactcattattaaaagttatgtgagcggtgttgt-tcgg--gttccagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG

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|13562782|gb|BG551002.1|BG551002
EST:     ACCAGGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAG                         GATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
genomic: ACCAGGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAGgtgtttatct ... gctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
EST: gi|22522391|gb|BU081202.1|BU081202
EST:     ACCAGGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAG                         GATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
genomic: ACCAGGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAGgtgtttatct ... gctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
EST: gi|151398683|gb|EV268554.1|EV268554
EST:     ACCAAGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAG                         GATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
genomic: ACCAGGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAGgtgtttatct ... gctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
EST: gi|18040842|gb|BM309136.1|BM309136
EST:     TTGATGGACAAG                         GATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
genomic: TTGATGGACAAGgtgtttatct ... gctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
EST: gi|20448926|gb|BQ253050.1|BQ253050
EST:     ACCAGGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAG                         GATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT
genomic: ACCAGGCCTTGGTTGGTGACAAGACAATTGCATTTTGGTTGATGGACAAGgtgtttatct ... gctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgcagtttgtcatttgacaaatattttactaatgttctgttggctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTG
                             tactaat  putative branch site (score: 1)
                                              ctgcttc  putative PPT
              atttgacaaatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtcaaatcatttaaggacacttgtgtttgctttataagtgtattgctgcagtttgtcatttgacaaatattttactaatgttctgttggctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTG

- - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - ttgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg