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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtagtttcaacataaaacatatttatgtgcagttttgccatccttcaaaagaagatagaaacttactccatgttactctgtctatatgtaatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTTATCCATCAC

Basic information

species Glycine max
transcript GLYMA18G06950.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G06950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 6
tggtagtttcaacataaaacatatttatgtgcagttt-tgccatccttcaaaagaagatagaaacttactccatgttactctgtctatatgtaat-ttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTTATCCATCAC-
   |     |   |||   | | |   | |  | ||  |    | || |  |  || |  |||| |    |        |||| | ||    | | ||  ||||||||||| || ||  | ||||| || ||||| || ||||| ||||| || |||||||||||||| ||||||||||||||||||||||| ||||| ||| 
-tatgagcactctatacttcctctcactctatacttcattaagttctgcttacaaacactgaaaatagggctgaaca--tctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC

upper sequence: GLYMA18G06950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g01370.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------------------------tggtagtttcaacataaaacatatttatgtgcagttttgcc--atccttcaaaa------gaagatagaaacttactcca----tgttactctgtctatatgtaat-ttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTTATCCATCAC-
                                                                           | | | | || | ||  |    | |||      | |  |   || |||||  |      |   | | | ||| |    |    ||    |||| | ||    | | ||  ||||||||||| || ||  | ||||| || ||||| || ||||| ||||| || |||||||||||||| ||||||||||||||||||||||| ||||| ||| 
gtatatcttttttctgtattgattggatcatagtttttccagaataaagcatgaaaagttgctgtaggttattgagttgggtgcagcctatgagcactctatacttcctctcactctatacttcattaagttctgcttacaaacactgaaaatagggctgaacatctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC

upper sequence: GLYMA18G06950.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------------------------------------tggtagtttcaacataaaacatattt---atgtgcagttttgc---------catccttcaaaaga-agatagaaacttactccatgttactctgtctatatgtaatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTTATCCATCAC-
                                                                     | ||  |  |   |||| | ||||     || ||   ||||         |||  |    |  |  ||||||  || |  |  |  |  ||  | | | ||  ||   |||||||||||| |||||| | || || || ||||| || ||||| |||||||| ||| | |||||||| |||||||||||||||||||||||||| |||||  
gtactgataaacaaagatatggtcagaacactaatttgagttcttggattcttaacttgatggttagctgcagcctgcaaccaaaatagatttcaggggtccaaccttgctgagaagtacattttatgtagaatggatagagcctaatgctttagttgtcattatgt-tggtatggaacagGAATGGAGCTATCTACGAGGAGGGCTAACAACGGTTGATCGTGACTATGGCTGGTTTAACAACATCCACCATGACATTGGCACCCATGTTATACATCATC

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|208242245|gb|GE036049.1|GE036049
EST:     TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGAGTTATCTAAGG
genomic: TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGG
EST: gi|208214786|gb|GE009323.1|GE009323
EST:     TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
genomic: TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
EST: gi|193411735|gb|FK378982.1|FK378982
EST:     TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
genomic: TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
EST: gi|208298438|gb|GE096215.1|GE096215
EST:     GCAGAAACTGTCCTTTGGTTACCGTGGCCA                         GGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
genomic: GCAGAAACTG-CC-TTGG-TACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
EST: gi|208170209|gb|GD968800.1|GD968800
EST:     ATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGNGTTNTCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
genomic: ATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
EST: gi|208066092|gb|GD866801.1|GD866801
EST:     TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
genomic: TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
EST: gi|208200572|gb|GD996937.1|GD996937
EST:     GCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
genomic: GCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
EST: gi|208317446|gb|GE114855.1|GE114855
EST:     CTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGAGTTATCTAAGGGGCGGTCTTACAACAGTAGATCGCGACTATGG
genomic: CTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
EST: gi|207823344|gb|GD795363.1|GD795363
EST:     TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
genomic: TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
EST: gi|208327605|gb|GE124129.1|GE124129
EST:     TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCA                         GGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG
genomic: TACTTGCATCATCATGGTTACAAGCAGAAACTGCCTTGGTACCGTGGCCAggtatcccat ... taatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaaagaagatagaaacttactccatgttactctgtctatatgtaatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTTATCCATCAC
                aacttac  putative branch site (score: 2)
                                     tctatatgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtagtttcaacataaaacatatttatgtgcagttttgccatccttcaaaagaagatagaaacttactccatgttactctgtctatatgtaatttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTTATCCATCAC

- - - - - - - -aaaacata
- - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtcta