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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttctcttatgtttattcttgtagagtcctactcctacacaagtttttacctatccgttgtacttatattgtgattttttcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGATGTCAAACCTGATAATATTTATGTGAAAAATGGTGTTTACAAGCTTGGTG

Basic information

species Glycine max
transcript GLYMA03G37010.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G37010.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G02970.1 (Arabidopsis thaliana), 3'ss of exon 8
gtctgtttctcttatgtttattcttgtagagtcctactcctacacaagtttttacctatccg-----ttgtacttatattgtgat--tttttcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGATGTCAAACCTGATAATATTTATGTGAAAAATGGTGTTTACAAGCTTGGTG
    ||      |   || ||| |  || |     |    || | |  || ||   | |  |     || ||   |||   |  |  | | ||     ||| | || || ||| | || ||| | || ||||| |||||||||||| ||||||| |||||||| ||||||||  | || || ||||||| |||||||||||
----gtaaacactggcttcattttcatataaaatcaagtatagagatattattgattctttgaattcttatatacataccattgtactatgtctcttacagATAGCAAAGGCATTACATTTTGTGCATGAGAAAGGAATAGCTCATTTAGATGTAAAACCTGACAATATTTACATTAAGAACGGTGTTTGCAAGCTTGGTG

upper sequence: GLYMA03G37010.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0104g01740.t01 (Vitis vinifera), 3'ss of exon 8
----gtctgtttctcttatgtttat----tcttgtagagtcctactcctacacaagtttttacctatccgttgta-cttatattgtgattttttcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGATGTCAAACCTGATAATATTTATGTGAAAAATGGTGTTTACAAGCTTGGTG
        || |||  |  |||||     || | || |   | |||   ||   |||||| |  |||   |   | ||| |    |||  |||   |   ||| ||||||| ||  ||||||||| ||| ||||| ||||||||||| |||||||| ||||||||||| |||||||| ||| ||||||||||||| |||||||
gataaatcgtatcttgtg-gtttaccatgtcatttaaatgtccactaggaccttagttttaagttattgttaacatcttttcacttgaactttgtcta--cagATTGCCAAGGCCTTGCAATTTACACATGAGAAAGGAATAGCTCACCTAGATGTAAAACCTGATAACATTTATGTCAAAGATGGTGTTTACAAACTTGGTG
















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|193694374|gb|FK629518.1|FK629518
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
EST: gi|193531199|gb|FK484150.1|FK484150
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCT
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCT
EST: gi|193520760|gb|FK479759.1|FK479759
EST:     CTTTATTTACAG-AGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTACAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: CTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
EST: gi|193614362|gb|FK565960.1|FK565960
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
EST: gi|193583750|gb|FK543734.1|FK543734
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
EST: gi|208110247|gb|GD907293.1|GD907293
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCTAATG
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCC-AATG
EST: gi|193528563|gb|FK486823.1|FK486823
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
EST: gi|208268144|gb|GE073003.1|GE073003
EST:     ATACTCCGTCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: ATACTCCG-CTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
EST: gi|193521030|gb|FK482451.1|FK482451
EST:     ACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: ACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
EST: gi|193326511|gb|FK289858.1|FK289858
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCT
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCT
EST: gi|193432827|gb|FK396571.1|FK396571
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATA
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATA
EST: gi|26058768|gb|CA801682.1|CA801682
EST:     AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: AATACTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
EST: gi|208039457|gb|GD836239.1|GD836239
EST:     CTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAG                         GTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT
genomic: CTCCGCTTTATTTACAGAAGGACAAGTGTTAGATGCCTTATTTCAGgtctgtttct ... tcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacacaagtttttacctatccgttgtacttatattgtgattttttcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGATGTCAAACCTGATAATATTTATGTGAAAAATGGTGTTTACAAGCTTGGTG
                                        ttttttcat  CT-rich tract
                             ttatattgtgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtttctcttatgtttattcttgtagagtcctactcctacacaagtttttacctatccgttgtacttatattgtgattttttcatgatcagGTTGCCAATGCACTGCAATTTATACACGAGAAGGGAATAGCTCATCTAGATGTCAAACCTGATAATATTTATGTGAAAAATGGTGTTTACAAGCTTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT