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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttatttatccctttctacctatcttgtatttcagtagttcaaatttgggtcaatattttagctaattttcttcaatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATGGCATTTAAGCTATTTCATGGGAAGGATGGAGTCATTCCCCTATCTGAGA

Basic information

species Glycine max
transcript GLYMA09G34650.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34650.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0033g01160.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------------gtgagttatt-tatccctttctacct-atcttgtatttcagtagttcaaatttgggtcaatattttagctaattttcttcaatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATGGCATTTAAGCTATTTCATGGGAAGGATGGAGTCATTCCCCTATCTGAGA
                                                                             ||  |    |||    |  | | | |  |||| | |       |  |||  | |  ||   ||  ||||  |||  ||  |  | |||| |  ||| |||  ||||| || || |||||||| || | |||||  |||||||||||||| ||||||||||||||||| ||  | || || || | ||
gtgagttgttattctcttttgttctctctgcctttttcttcttgattttgtatagtcttttccccgtactaatgctagaactgcaatatgatatggtccttgaatttgtctgttgtcttctgtaatacgagaaaacccttatgctatcttttgtc--tcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATGGCATTTAAGCTCTTTCATGGGAAGGATGGGGTTGTCCCACTCTCAGGGA
















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|151395813|gb|EV265690.1|EV265690
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|9987491|gb|BE661599.1|BE661599
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|209720586|gb|BW654439.1|BW654439
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|20812607|gb|BQ297085.1|BQ297085
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|27426597|gb|CA938117.1|CA938117
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|151400423|gb|EV270237.1|EV270237
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|298167526|gb|HO012789.1|HO012789
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|24205459|gb|BU964712.1|BU964712
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|38192748|gb|CF921954.1|CF921954
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|14999869|gb|BI320683.1|BI320683
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|20812455|gb|BQ296933.1|BQ296933
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
EST: gi|15288136|gb|BI472027.1|BI472027
EST:     TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCT                         GTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG
genomic: TCAATGAACCTACAAACTTCTCTTTCTCCTCAACTAAAATCTCCATTCCTgtgagttatt ... caatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcagtagttcaaatttgggtcaatattttagctaattttcttcaatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATGGCATTTAAGCTATTTCATGGGAAGGATGGAGTCATTCCCCTATCTGAGA
                                agctaat  putative branch site (score: 3)
                                      ttttcttc  CT-rich tract
                        aatattttagctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttatttatccctttctacctatcttgtatttcagtagttcaaatttgggtcaatattttagctaattttcttcaatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATGGCATTTAAGCTATTTCATGGGAAGGATGGAGTCATTCCCCTATCTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA