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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacagtttggtcattttttcctttatttctttcattaattgcagttacttttctcttatctttgtgcattgctgactacatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG

Basic information

species Glycine max
transcript GLYMA07G03930.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 18
gtgagaacagtttggtcattttttcctttatttctttcattaattgcagttacttttctcttatctttgtgcattg-ctgactacatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG
|| |||  |    | | | | ||       |||  | |||| ||     | |   | | |  ||| |  |  ||   ||   | | |  ||||| || | |||||| || || ||  ||||  |||| || ||||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||
gtaagataaagacgcttaatattaatgcccttttgtacattcatcatcatcatcatcccc--atcctcattgatgaactctgttcttttgcagCCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG
















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|192309363|gb|FK000571.1|FK000571
EST:     CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTT                         TTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTT
genomic: CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTTgtgagaacag ... acatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTT
EST: gi|22927461|gb|BU544600.1|BU544600
EST:     CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTT                         NNGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTT
genomic: CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTTgtgagaacag ... acatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTT
EST: gi|298165294|gb|HO011343.1|HO011343
EST:     CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGATGGATCTT                         CTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTT
genomic: CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTTgtgagaacag ... acatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTT
EST: gi|192309362|gb|FK000570.1|FK000570
EST:     CTGTGCAATCATCAATCCTCCTCAG-CTGGCATTCTTGCCGTTGGATCTT                         CTGAGAGGAGGGTCGTTCCGGGTTCAG-TGCTGAAGAGTTCAAGTTTGCTT
genomic: CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTTgtgagaacag ... acatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTT
EST: gi|8827585|gb|BE211315.1|BE211315
EST:     CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTT                         CTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTATGCTT
genomic: CTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTTgtgagaacag ... acatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaattgcagttacttttctcttatctttgtgcattgctgactacatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG
                                     tgctgac  putative branch site (score: 2)
            ttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaacagtttggtcattttttcctttatttctttcattaattgcagttacttttctcttatctttgtgcattgctgactacatgagcagCTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG