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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggtgccattaaagggcatgatgcgtgtttttcttctaaatccaaaatgcaccactatctggtgaactatgatgggattgacttgaaacgattcactgcttttttcttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCACCAGCTCCAAG

Basic information

species Glycine max
transcript GLYMA08G02940.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 6
gtacggtgccattaaagggcatgatgcgtgtttttcttctaaatccaaaatgcaccactatctggtgaactatgat--gggattgacttgaaacgattca---ctgcttttttcttaata-cagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCACCAGCTCCAAG
                                     ||| ||| ||||   ||      |      |  | || |  || ||||   | |    | |        ||  | |||||| | |||||||| |||||||| ||||||||||||||||| || || |  || ||||||||||||||   |||||| || |||||||||||
----------------------------------gtatctgaatgcaaacctcaatcaagttctacaagttctgttttggaattgttgtaatctcactggggttctctcctatcttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAATTTGATCTTAATGGAATCCCTCCAGCTCCAAG
















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|254328820|gb|GR833192.1|GR833192
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|254336018|gb|GR841343.1|GR841343
EST:     CTACCAGGACCAGCAGACTA-CGTCT-CATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|17518873|gb|BM187915.1|BM187915
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|254328819|gb|GR833191.1|GR833191
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|15285743|gb|BI469634.1|BI469634
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|18734607|gb|BM528280.1|BM528280
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|9258803|gb|BE346950.1|BE346950
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|192328286|gb|FK022920.1|FK022920
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|193371490|gb|FK333713.1|FK333713
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|192300936|gb|FG992996.1|FG992996
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|7232353|gb|AW567710.1|AW567710
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|13180745|gb|BG352085.1|BG352085
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|207811998|gb|GD783583.1|GD783583
EST:     TCAAGTGTTCACCACCTATCAGGACCAGCAGACTACCGTCTCCATTCTAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAA
genomic: TCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTC-AGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAA
EST: gi|7235265|gb|AW570594.1|AW570594
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTACATTCAT                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|193337800|gb|FK302111.1|FK302111
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
EST: gi|7235257|gb|AW570586.1|AW570586
EST:     CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAG                         GTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA
genomic: CTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgcc ... cttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgaactatgatgggattgacttgaaacgattcactgcttttttcttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCACCAGCTCCAAG
                                            tcttaat  putative branch site (score: 3)
                               ttcactgcttttttct  CT-rich tract
                                       ttttttcttaataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggtgccattaaagggcatgatgcgtgtttttcttctaaatccaaaatgcaccactatctggtgaactatgatgggattgacttgaaacgattcactgcttttttcttaatacagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCACCAGCTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC