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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaactggtctttttaagtaaaaaaatgtgtatattttagtggaagccaggtgaaccttcacattggcttatatattttttctctctttggcatacagGTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATCGTTACCGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

Basic information

species Glycine max
transcript GLYMA05G30210.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 10
ttgaaactggtctttttaagtaaaaaaatgtgtatattttagtggaagccaggtgaaccttcacattgg--cttatatattttttctc-tctttggcatacagGTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATCGTTACCGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
 | |||| ||      ||| |     |   |  |   || | |     | | |    |||     |||   |||||  ||  || ||  || |      ||||||||||||||| ||||| || ||| ||||||||||| |||| || || || || ||| | ||||| ||||| || || ||||| ||  || | ||||| |
gtaaaacaggcaacactaattttccca---tacaggcttcatta----ctaaggagccctgagagttgagacttatgcatccttcctgatcatctattgacagGTGTACTATGTATATGGGTTCATGTTGCTAGTCTTTTTGATCCTCATAATTGTCACCATCTGTGTAACAATCGTTGGTACATATTTCCTGCTGAATGCGG

upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 10
ttgaaactg-gtctttttaagtaaaaaaatgtgtatattttagtggaagccaggtgaaccttcacattggcttatatattttttctctctttggcatacagGTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATCGTTACCGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
 | |  ||  ||  |||||    | |     | || ||||  |  ||       ||   ||| |  ||    |     ||| |  | | | ||    |||||| || ||||| |||||||||||| |||| || ||  |||||||||| || ||||| || ||||| ||||||||||||||||| || ||||| |||||||
-taattctctgttcttttattggagatgccatttaaatttatgctgactgtgtttgtggcttaatcttattatgctgctttgtgatttttgtgctcaacagGTATATTATGTATATGGCTTTATGTTGCTTGTTTTCATGATTCTTATGATTGTTACAGTCTGTGTAACAATTGTGGGGACATATTTCTTGTTGAATGCTG

upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 10
-ttgaaactggtctttttaagtaaaaaaatgtgtatattttagtggaagccaggtgaaccttcacattggcttatata---ttttttctctctttggcatacagGTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATCGTTACCGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
 |         | ||||| || ||       | | | ||| |  |||   ||  |     ||  || ||| | ||| |   ||||| || | | ||     |||||||| ||||| |||||||||||||| || || || |||||||| || || || || |||||||||||||| ||||| |||||||| ||| |||||||||
ctctctctctctatttttgagaaattcggactat-tgtttgacaggagttcaaattg---tttgcagtggatgataaacattttttgctgtttgtgctgggcagGTGTATTATGTCTATGGCTTTATGCTACTGGTTTTCCTGATTCTCATAATTGTCACTGTTTGTGTGACAATAGTGGGAACATACTTCTTGCTAAATGCTG

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|193403010|gb|FK367276.1|FK367276
EST:     GCATATTCATTGAAATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATC
genomic: GCATATTCATTGAAATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaatcaca ... tggcatacagGTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATC
EST: gi|208294361|gb|GE092178.1|GE092178
EST:     GCATATTCATTGAAATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATC
genomic: GCATATTCATTGAAATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaatcaca ... tggcatacagGTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagccaggtgaaccttcacattggcttatatattttttctctctttggcatacagGTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATCGTTACCGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
                        cttatatattttttct  CT-rich tract
                         ttatatattttttctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaactggtctttttaagtaaaaaaatgtgtatattttagtggaagccaggtgaaccttcacattggcttatatattttttctctctttggcatacagGTGTACTATGTGTATGGCTTTATGCTGCTAGTCTTTCTGATTCTTATCATCGTTACCGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttcac