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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctattcaccattagtttgtgcctttaccactctttgcgattttcaaatgagattcatactgaaacacttttcactcaaatgtacaatattgaaga...

Basic information

species Glycine max
transcript GLYMA08G38990.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G38990.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 5'ss of exon 12
GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtat-gctattcaccattagtttgtgcctttaccactctttgcgat-tttcaaatgagattcatactgaaacacttttca---ctcaaatgtacaatattgaaga--------------------------------------------
||| || |||||  | || || || || ||  |||| ||||||||||| ||||| ||||||||||| || |||||||| ||||||  |   ||     ||  || |  |    |||     |||     ||||| ||    |   |     |  |||| ||     || |  || |    ||  | |                                            
GTATGTGTTTGGGCTCACCCATATCCCAAGGCTGGAGGACTGGCCTGTCATGCCAGTGGAACGCATCGGCTTCATGCTCATGgtaaagacctttttttttttttagaacaaagaccttctcttgtagcctttcatatctcctctttggcagacgacttctctagtttccaccgttctggtttttacagtatcagctcaaagcctgtttgtgtcttgtttaattcttttcag

upper sequence: GLYMA08G38990.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgct-attcaccatt-agtttgtgcctttaccactctttg---cgatt-ttcaaatgagattcatactgaaacacttttcactcaaatgtacaatattgaaga
||| |||||||||||||||||||||||| |  |||||||||||||||| ||||| ||||| | ||||||||| | ||| |||||||  | || || |||| |   |     |||   |  || |    | ||| ||||  ||||     |  |  ||||   |   ||    |  |   |  | |   
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcatttaacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctt---tccatgctcctaa---

upper sequence: GLYMA08G38990.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S9_129V6.2 (Physcomitrella patens), 5'ss of exon 6
GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctattcaccattagtttgtgcctttaccactctttgcgattttcaaatgagattcata---ctgaaacacttttcactcaaatgtacaatattgaaga------------------------------------------------------
||| ||||||||||| || ||||| |||||| ||||||| ||||| |||||||| ||||| | |||||| ||||   |  ||||  |   |  |||  | || | |         |      |   ||   ||||   |  |||    |||   |  ||    ||   ||    | | || |  |                                                      
GTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTGgttag---tgtacctcttgtctatatacccgaaagctagagtccttgaaaaattctacccattggtctgtttctgttgaatcttggataagtagtcttaagtacttctgaagccgtgcactaacatagaaaaattgactggttttgatctggtacag

upper sequence: GLYMA08G38990.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 5'ss of exon 13
GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgc-tattcaccattagtttgtgcctt-taccactctttgcgat---------tttcaaatgagattcatactgaaacacttttcactcaaatgtacaat--attgaaga-----------------------------------
||| ||||||||||| || |||||||||||| | ||||||||||| || ||||| ||||| | |||||| ||||   | |||||  |  | |    | |  ||||   ||||  || |  |  ||| |          || |  ||   | |  |  | ||  |  ||  |  || |||  | ||  ||   | |                                   
GTATGTATTTGGAGTTACTCACATTCCTAGACTTGAAGACTGGCCAGTAATGCCTGTGGAGCACATTGGATTCAGTTTGATGgtgagtatgtctgtcgt--gtttaaaccttgcactatgcactgcaacagtaagaccttgcttattgaactgtttttaaagaatcttagatacacatgctccattcatctgaaacagtggtataatatggttgcgttgttttgatacag

upper sequence: GLYMA08G38990.1 (Glycine max), 5'ss of exon 11
lower sequence: EFJ13052 (Selaginella moellendorffii), 5'ss of exon 10
GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctattcaccattagtttgtgcctttaccactctttgcgattttcaaatgagattcatactgaaacacttttcactcaaatgtacaatattgaaga
|||||||||||||||||||||||| |||||  | || || ||||| || ||||| ||||| ||||| || ||||  || | |||| |  | ||  |  | | |||   || |  | |   |  ||| |     |||     |  |                                     
GTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACGgtagg--aatcctcgatcgcttg---ctatggcgccgctaacgagtgatcgatggatcgcgcag------------------------------------

upper sequence: GLYMA08G38990.1 (Glycine max), 5'ss of exon 11
lower sequence: EFJ14061 (Selaginella moellendorffii), 5'ss of exon 10
GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctattcaccattagtttgtgcctttaccactctttgcgattttcaaatgagattcatactgaaacacttttcactcaaatgtacaatattgaaga
|||||||||||||||||||||||| |||||  | || || ||||| || ||||| ||||| ||||| || ||||  || | |||| |  | ||  |  | | |||   || |  | |   |  ||| |     |||   | |  |                                     
GTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACGgtagg--aatcctcgatcgcttg---ctatggcgccgctaacgagtgatcgatggattgcgcag------------------------------------

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|213603176|gb|DB981030.1|DB981030
EST:     TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG                         CCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA
genomic: TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctatt ... tgatatgcagCCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA
EST: gi|19934738|gb|BQ079768.1|BQ079768
EST:     TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG                         CCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGCTCCACCAAACCAA
genomic: TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctatt ... tgatatgcagCCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA
EST: gi|58017921|gb|CX704663.1|CX704663
EST:     TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG                         CCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA
genomic: TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctatt ... tgatatgcagCCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA
EST: gi|120529727|gb|EH257861.1|EH257861
EST:     TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG                         CCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA
genomic: TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctatt ... tgatatgcagCCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA
EST: gi|19347415|gb|BM892295.1|BM892295
EST:     TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG                         CCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA
genomic: TGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctatt ... tgatatgcagCCGCATGGGTTTTTCAATTGCTCGCCTGCTGTTGATGTTCCACCAAACCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgctattcaccattagtttgtgcctttaccactctttgcgattttcaaatgagattcatactgaaacacttttcactcaaatgtacaatattgaaga

- - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - -  GGAAGA