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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatgatcacctagtgcagtacgcatatgattctggaatcatttagtcttttttttttttttttgcattactgtccactcatttgtttatgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG

Basic information

species Glycine max
transcript GLYMA20G35600.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 3'ss of exon 8
tcaatgatcacctagtgcagtac-gcatatgattctggaatcatttagtcttttt--tttttttttttgcattactgtccactcatt-----tgtttatgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG
|| ||| | | | || || | | || || ||| || | | | || |||| || | | | | || ||| || ||||| || |||||| | ||||||||||| |||||||| || |||||||| | |||||||| || ||||||||
--------tgcccagtaaaaccttgagtttgtttttctactcgttcagtgcttgtggtatgcacacatggattaacttcaattgtataatggtcttcatgccatacagATAGATACAAAGGACATTCTTTTTATTTGTGGTGGTGCTTTTATTGACTTGGAGAAAACTATATCAGAGAG

upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 8
tcaatgatcacctagtgcagtacgcatatgattctggaatcatttagtcttttttttttttttttgcattactgtccactcatt---tgtttatgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG
|| || | | ||| | | || |||| | | | || ||| ||| | || | | ||| | || |||| ||||||| || ||||| |||| |||||||||||||||||||||||| ||||| | || |||||||||||||| ||
---attttccttcatctgattactatcaattctacatcattatttcatgatagctgttgctttgctaatttcgttctaataattacattttaatgaattgcagATAGATACAAAAGATATCCTTTTTATATGTGGTGGAGCATTTGTTGATTTAGAAAAAACCATTTCAGATAG

upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S171_84V6.1 (Physcomitrella patens), 3'ss of exon 8
tcaatgatcacctagtgcagtacgcatatgattctggaatcatt-tagtcttttttttttttttttgcattactgtccactc-atttgtttatgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG
||| | | | | | |||| | || || | | | ||||| | | || | || || | |||||||||||| || ||| |||||||||| |||||||| || || ||||| || |||| |||||| || ||||| |
--catggtgggtttctatacccaggttatgtcttctctgctatcgtaacatggcagcatctattttggctagacatttacctgagcagtgtaagttatgcagATTGATACCAAGGATATTCTTTTCATATGTGGAGGTGCTTTTATCGAACTTGCGAAAACTGTTGCAGAGCG

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|193357635|gb|FK320201.1|FK320201
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|208311212|gb|GE102988.1|GE102988
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|193344284|gb|FK312814.1|FK312814
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|193456440|gb|FK421786.1|FK421786
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTANATGTGGTGGAGCATTTATTGA
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGA
EST: gi|193425329|gb|FK388602.1|FK388602
EST:     CGTTCCTGAGAGAGGAGCAAGGAAGCATTCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: CGTTCCTGAGAGAGGAGCAAGGAAGCA-TCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|17519864|gb|BM188906.1|BM188906
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|193354939|gb|FK322548.1|FK322548
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|193339490|gb|FK302737.1|FK302737
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|207809763|gb|GD781837.1|GD781837
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|193361573|gb|FK324355.1|FK324355
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
EST: gi|193400816|gb|FK368737.1|FK368737
EST:     ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAG                         ATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT
genomic: ACGTTCCTGAGAGAGGAGCAAGGAAGCATCCACGGGGTGATAACATACAGgtatgttgtt ... tgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcttttttttttttttttgcattactgtccactcatttgtttatgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG
     tttttttttttttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatgatcacctagtgcagtacgcatatgattctggaatcatttagtcttttttttttttttttgcattactgtccactcatttgtttatgatatgcagATTGACACAAAGAATATTCTTTTTATATGTGGTGGAGCATTTATTGATCTTGAGAAAACCATTTCAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - -ctagtgc
- - - - - - - - - -gtacgca
- - - - - - - - - - - - - - -gattctg