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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcaagctggtcttgtatcaggttacctcaatggaagtatttctgttattttaatgattcaaacatgttgaattgatatattgacattcctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCAAAAACCTATATTTTCCTGCATTTGCCTCAG

Basic information

species Glycine max
transcript GLYMA15G05740.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05740.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 10
attcaagctggtcttgtatcaggttacctcaatggaagtatttctgttattttaatg-attcaaacatgttgaattgatatattgacattc--ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCAAAAACCTATATTTTCCTGCATTTGCCTCAG
| ||  || ||  ||  |     |||| ||   | || |   | |   || ||  |   |||   | |||    ||| |  | ||| |||    || |  ||||| || |||||||||||||| || |||||||||  |||||| ||| ||||||| | ||| || ||||||||||| || |||
actc--gcagggtttaaagttatttacttctgcgtaaatggat-taccatgttggtttgttctgtcctgtaagcttgtttcactgaaatttgtttgtttatagGTGTGTTATGACTGGAGTAAGGGTGCAGAAAATCATAATCCAGCAACAGCAAAGAGCTACATCTTCCTGCATTTACCACAG
















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|8670273|gb|BE191380.1|BE191380
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|18848529|gb|BM567714.1|BM567714
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCT
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCT
EST: gi|24205294|gb|BU964547.1|BU964547
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GCCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|16106332|gb|BI894072.1|BI894072
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|21887065|gb|BQ740278.1|BQ740278
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|254327975|gb|GR834940.1|GR834940
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|254327974|gb|GR834939.1|GR834939
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|21887213|gb|BQ740426.1|BQ740426
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|8670281|gb|BE191388.1|BE191388
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|15200978|gb|BI424629.1|BI424629
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|13311248|gb|BG404881.1|BG404881
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAAAATNCTAATCCTGCAGCAACA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCA
EST: gi|15000181|gb|BI320995.1|BI320995
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA                         GTCTGCTATGACTGGAGTAAAGGGGCAGAA
genomic: CTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccac ... ctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttattttaatgattcaaacatgttgaattgatatattgacattcctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCAAAAACCTATATTTTCCTGCATTTGCCTCAG
                                  tattgac  putative branch site (score: 2)
                                          ttcctgctc  CT-rich tract
                       ttgaattgatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcaagctggtcttgtatcaggttacctcaatggaagtatttctgttattttaatgattcaaacatgttgaattgatatattgacattcctgctcgtagGTCTGCTATGACTGGAGTAAAGGGGCAGAAAATTCTAATCCTGCAGCAGCAAAAACCTATATTTTCCTGCATTTGCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-ttcaagc
- - - - - - - - - - - - -acctcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacattc