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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAGCTCCTGCTCGTGTTGGTTTGGTTGCCCCAATTGATGTTGTTGTTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatcttctgtttgtagaatttgggggtggttgatttgttttggtttttaaaaactattaatattttaaatattacgttgagtagaagtggggaa...

Basic information

species Glycine max
transcript GLYMA14G06630.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G06630.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S39_424V6.1 (Physcomitrella patens), 5'ss of exon 2
-GTTGGAGCTCCTGCTCGTGTTGGTTTGGTTGCCCCAATTGATGTTGTTGTTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatcttctgtttgtagaatt-tgggggtggttgatttgttttggtttttaaaaact-attaatattttaaatattacgttgagtagaagtggggaa----
 || ||||||||||| ||||| ||| | |||||||| ||||||||  |||| |||||||||||||| || || |||||||| ||||| ||||||||||||||  |   |    |         ||    |   |  |   ||     ||   | | | |  |  |  |  ||     | | ||      |    || |   |    
GGTCGGAGCTCCTGCGCGTGTGGGTCTTGTTGCCCCCATTGATGTGATTGTACCTCCTGGCAACACTGGTCTGGATCCCTCTCAGACTTCTTTCTTCCAGgtgagatttaaattacgcacttgatggcagatatcatgttttcacagtgacatctgatattttgtccactttccgtttctgacacctgatgcgtgttgattatcag

upper sequence: GLYMA14G06630.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S38_196V6.1 (Physcomitrella patens), 5'ss of exon 2
-GTTGGAGCTCCTGCTCGTGTTGGTTTGGTTGCCCCAATTGATGTTGTTGTTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgt--------tggta-atcttctgtttgtagaatttgggggtggttgatttgttttggtttttaaaaactattaatat-----tttaaatattacgttgagtagaagtggggaa------------------------------------------------
 || ||||| ||||||||||| |||||||||||||| || ||||| |||||||| || || ||||| || || |||||||| ||||| ||||||||||||||         |||| ||  | ||||    ||||  |      ||   |   ||| | || |   |       | | |     ||   || |     |   | | |||   |||                                                
GGTCGGAGCACCTGCTCGTGTGGGTTTGGTTGCCCCCATCGATGTGGTTGTTCCCCCCGGTAACACTGGTCTGGATCCCTCGCAGACATCTTTCTTCCAGgtaaggtcttcggtatatggtatgttctatgaatgagattccagtcagtcaatttagcttatcgcagtgggcaagtgtcctttttctgatgtcgttctttatggcagttatgaaacgctgttaactgaaggtttctgacgaatagaatgctgaactctccag

upper sequence: GLYMA14G06630.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ13245 (Selaginella moellendorffii), 5'ss of exon 3
GTTGGAGCTCCTGCTCGTGTTGGTTTGGTTGCCCCAATTGATGTTGTTGTTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatcttctgtttgtagaatttgggggtggttgatttgttttggtttttaaaaactattaatattttaaatattacgttgagtagaagtggggaa
|||||||| ||||||||||| ||  | |||||||| || || ||     |||||||||| | ||| ||||| |||||||| ||||| |||||||||||||||    | | ||| ||| |    |||     | |||  | || ||   |  ||  |||||   |                                   
GTTGGAGCGCCTGCTCGTGTCGGACTTGTTGCCCCGATCGACGTAACCATTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgtt--cgaccctcttttttt----ttttttttttgtttctgtggttca-tacttgcaaacttccag----------------------------------

upper sequence: GLYMA14G06630.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ24514 (Selaginella moellendorffii), 5'ss of exon 3
GTTGGAGCTCCTGCTCGTGTTGGTTTGGTTGCCCCAATTGATGTTGTTGTTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatcttctgtttgtagaatttgggggtggttgatttgttttggtttttaaaaactattaatattttaaatattacgttgagtagaagtggggaa
|||||||| ||||||||||| ||  | |||||||| || || ||     |||||||||| | ||| ||||| |||||||| ||||| |||||||||||||||    | |       ||     |||    |||||| ||   |      ||  |                                             
GTTGGAGCGCCTGCTCGTGTCGGACTTGTTGCCCCGATCGACGTGACCATTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgtt--cgaccaaagaggtgctctgtttct--gtggttcatacttgcaaacttccag--------------------------------------------

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|24135677|gb|BU926187.1|BU926187
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|16346828|gb|BI972423.1|BI972423
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAAGGG-ACTGTTGAAATCATTAC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAA-GGGTACTGTTGAAATCATTAC
EST: gi|7685264|gb|AW755912.1|AW755912
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|16347968|gb|BI973563.1|BI973563
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|254328265|gb|GR835230.1|GR835230
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|254333170|gb|GR850420.1|GR850420
EST:     TTCCTGCTGGCAACACAGGGCTCGATCCCGCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|19347127|gb|BM892007.1|BM892007
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|254339096|gb|GR847813.1|GR847813
EST:     -TCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|14990690|gb|BI316363.1|BI316363
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|151409120|gb|EV278928.1|EV278928
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|7590329|gb|AW706084.1|AW706084
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|21677858|gb|BQ630209.1|BQ630209
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCTTACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|16104950|gb|BI892690.1|BI892690
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|7235180|gb|AW570509.1|AW570509
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTGCAG                         GTGCTCAACATTCCTACCAAGATTAACAAAGGTACTGTGGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|6483223|gb|AW202399.1|AW202399
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|192330815|gb|FK023044.1|FK023044
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACC
EST: gi|7685643|gb|AW756291.1|AW756291
EST:     TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAAACCTCTTTCTTCCAG                         GTGCTCAACATTCCTACCAAGATTAACAAGGGTACGTGTTGAAATCATTAC
genomic: TTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatc ... tgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTAC-TGTTGAAATCATTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGAGCTCCTGCTCGTGTTGGTTTGGTTGCCCCAATTGATGTTGTTGTTCCTCCTGGCAACACAGGGCTCGATCCCTCCCAGACCTCTTTCTTCCAGgttggtaatcttctgtttgtagaatttgggggtggttgatttgttttggtttttaaaaactattaatattttaaatattacgttgagtagaagtggggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgggga