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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcccttttcaactgtaagctaatgggcctgagtctatagctagtcccttcaagaactggacatctattatatctgatatcaaataatgctatgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTTGAAGCAACTTGATG

Basic information

species Glycine max
transcript GLYMA08G19640.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
--------------------------------gtttgcccttttcaactgtaagctaatgggcctgagtctatagctagtcccttcaagaactggac----atctattata-tctgatatcaaataatgctat---gctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTTGAAGCAACTTGATG
                                 |||       | ||  |    |   |  |  |   | | | |     |  | ||| |  |  |     || |||  || |||  ||| || |  |  |||   |  |||||||||||||||| |  |||||||||||| |||||||| ||| || | |     ||||||  ||||||| |  ||  |||  |  ||||  |    | |   |
gtcgctttacttctttgcatcattctgcacctttttttatccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactcttttatgaactggtcttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG

upper sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G102475_T02 (Zea mays), 3'ss of exon 8
----------------------------------gtttgcccttttcaactgtaagctaatgggcctgagtctatagctagtccc----ttcaagaactggacat-ctattatatctgat--atcaaataatg-ctatgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTTGAAGCAACTTGATG
                                    ||   |     |  || || |        ||     || ||||  | |     || | | | |     | || |    | ||||  |||   || |  || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | |     |||||||  ||    ||                                
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattttcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATT--------------------------------

upper sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G810275_T02 (Zea mays), 3'ss of exon 8
-----------------------------------gtttgccct-----tttcaactgtaagctaatgggcctgagtctatagcta-gtcccttcaagaactggac-atctattatatctgatatcaaataatgctatgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTTGAAGCAAC-TTGATG-
                                   ||| | ||      ||  |||    |  |  |   | | ||    |  | | ||   | ||  || |  || ||||  | |   |||| |   ||  | || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | |     |||||||  || ||  | |||   | | |  ||||  |  | | ||  || 
gtagctttgctgctttgcatcattcttcattttgagttagacccaaaaattggaacccccattttctttacataagctgtttcccatgtttgtgcagtaattctactatcttgtttgaatgatctgttatttt-ctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATT-CTAATTATGCAGACT-TGATGTTTGATAACCATTAGTGT

upper sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G102475_T01 (Zea mays), 3'ss of exon 8
----------------------------------gtttgcccttttcaactgtaagctaatgggcctgagtctatagctagtcc----cttcaagaactggacat-ctattatatctgat--atcaaataatg-ctatgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTT-CATGTGAATTGTAGTGTTGAAGCAACTTGATG
                                    ||   |     |  || || |        ||     || ||||  | |     || | | | |     | || |    | ||||  |||   || |  || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | |     |||||||  ||    ||  |||   |    |   ||||      ||  | 
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattttcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT-

upper sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 9
gtttgcccttttcaactgtaagctaatgggcctgagtctatagctagtcccttcaagaactggacatctattatatctgatatcaaataatgctatgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACA-TTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTTGAAGCAACT-TGATG---------------------------
                                                                                                                         ||||||||||||||||||||||| ||||||| ||||||||||||||||||||||||||| ||   ||||||||||||||| |||                             
-------------------------------------------------------------------------------------------------------------------------gtccaaaagtgtccatattcacaattttattgagacgaagataagtttctgttcatgtgcat---agtgttgaagcaactgtgaccatttcctgcttctttgcagGATCTTAG

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|208116357|gb|GD920380.1|GD920380
EST:     CTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAAG                         GTTATTTTTAATTT
genomic: CTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAAGgtttgccctt ... tgctctgcagGTTATTTTTAATTT
EST: gi|13311761|gb|BG405412.1|BG405412
EST:     CTGTTTCTTCAGTGGAGTGAGCATCGT-AAAGACTAAGCAATTTTATAAG                         GTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGAC
genomic: CTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAAGgtttgccctt ... tgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGAC
EST: gi|193492048|gb|FK453464.1|FK453464
EST:     CTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAAG                         GTTATTTTTAATTTTGGTCCAAAAGTGTCC
genomic: CTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAAGgtttgccctt ... tgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaagaactggacatctattatatctgatatcaaataatgctatgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTTGAAGCAACTTGATG
                        atctgat  putative branch site (score: 4)
                  tattatatctgatatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcccttttcaactgtaagctaatgggcctgagtctatagctagtcccttcaagaactggacatctattatatctgatatcaaataatgctatgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTTGAAGCAACTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA