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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatagaagttgtactactatcctttaccattatgcttgtattctgcttattatggctgttccatatttgccattctgacattacttatttgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT

Basic information

species Glycine max
transcript GLYMA06G17930.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17930.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 3'ss of exon 6
agatagaagttgtactactatcctt--taccattatgcttgtattctgcttattatggctgttccatatt-tgccattctgacattacttatttgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT
 |   |    |  | ||   | |||  ||| | | | || || || ||||| |  | | |     | ||| || |||    | || ||   | | |||   |||||| ||||| || ||||| ||||||||||||||| ||||||| ||| | || ||||| ||||| || || || ||||||| ||| ||||||||  |  |
-gtatgttactacattaaatttcttcctacgaatgtact-gtcttttgcttttgctagtttggttagattgtgacatgaatatat-accactgtttgc---agCCAAGCTTGTCCCGGTTGGTTACGGTATCAAGAAATTGCAAATCATGATGACCATTGTCGATGATCTTGTGTCGGTTGATAGTCTGATTGAGGACTACTT

upper sequence: GLYMA06G17930.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g29260.1 (Oryza sativa), 3'ss of exon 6
agatagaa----gttgtactactatcctttaccattatg-cttgtattc-tgcttattatggctgttccatatttgccattctgacattac-ttatttgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT
  ||   |     || | | | | |  | | | | ||   |  ||| |  |   |  | |    |||  ||| ||    |||| |||| |  | |||| |||   ||||||||||||||| ||||| || || ||||||||  ||||||||||| | || |||||||| || || |||||||| || | ||| ||||||||  || |
gtatgtgactctattcttcaattttattctgctaataaatccagtactaatatgtgctcttatggtttaatagttcattttctaacataaaatcatttttgc---agCCAAACTTGTACCAGTTGGATATGGCATCAAGAAGTTGCAAATTATGATGACCATTGTGGACGATCTTGTTTCTGTGGACAGTCTCATTGAGGATTATTT

upper sequence: GLYMA06G17930.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G031545_T01 (Zea mays), 3'ss of exon 6
--agatagaagttgtactactatcctttaccattatgcttgtattctgcttattatggctgttccatatttgccattctgacattacttatt-tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT
  |  |       ||  | |   | || |         |  |   ||  || || |  |  ||   |||      |   |  |  |  || |        ||||||| ||||| || ||||| || ||||||||||| |||||||| ||| | || || || || ||||| || ||||| || ||||| ||||||||  ||||
gtatgttacctcagttttccgcgcattaatttagtcattcatgaacttgtttttttaaccatttagtatggtttgtgacgtgaacatctactgccctttgcagCCAAGCTTGTCCCAGTTGGATATGGTATCAAGAAGCTGCAAATCATGATGACCATCGTCGACGACCTTGTCTCTGTCGACACTCTCATTGAGGACTATCT

upper sequence: GLYMA06G17930.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 6
agatagaagttgtactactatcctttaccattatgcttgtattc--tgcttattatggctgttccatatttgc-cattctgacattacttatttgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT
   |    |   |  |  || | ||||  | |      | |  |   |   ||||  |   |   ||  | |  || ||| |  ||| || ||| ||   |||||||||||||||| ||||| || ||||| |||||| |||| ||||||||||| |||||||| ||| | |||||||| ||    ||||||||||||||  |
--ttttgtgccctgtttttaacttttattactcgtaaggcaaacatcggagattaaagtaatattattctggaacaatctaattttaattgttt-tgttgcagCCAAACTTGTACCAGTTGGATATGGTATAAAGAAATTGCAGATTATGCTTACCATTGTGGACGACTTGGTTTCTGTGGACGACCTTATTGAGGAACAGTT

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|254336730|gb|GR842909.1|GR842909
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|12773256|gb|BG238183.1|BG238183
EST:     GAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGNGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTT
genomic: GAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGG-GGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTT
EST: gi|6072821|gb|AW102208.1|AW102208
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|254335479|gb|GR847007.1|GR847007
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|254329001|gb|GR833373.1|GR833373
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|6070838|gb|AW100225.1|AW100225
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|192294574|gb|FG986423.1|FG986423
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|8285537|gb|BE023096.1|BE023096
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|254343730|gb|GR857486.1|GR857486
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|193327735|gb|FK295492.1|FK295492
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGG-TACGGTATCAAGTAAACTGCAAATTATGCTT
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAG-AAACTGCAAATTATGCTT
EST: gi|57575395|gb|CX548370.1|CX548370
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|57575104|gb|CX548079.1|CX548079
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|254346824|gb|GR856546.1|GR856546
EST:     GAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: GAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|254329000|gb|GR833372.1|GR833372
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|254343731|gb|GR857487.1|GR857487
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|193302963|gb|FK266613.1|FK266613
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|21887772|gb|BQ740985.1|BQ740985
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|26269428|gb|CA820491.1|CA820491
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|213596126|gb|DB977488.1|DB977488
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|151403128|gb|EV272938.1|EV272938
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|151400262|gb|EV270076.1|EV270076
EST:     CAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|209728947|gb|BW655001.1|BW655001
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|16342208|gb|BI967803.1|BI967803
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|14990691|gb|BI316364.1|BI316364
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|23734643|gb|BU765560.1|BU765560
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|192296995|gb|FG990296.1|FG990296
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
EST: gi|6726934|gb|AW311214.1|AW311214
EST:     CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT                         CCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA
genomic: CGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATgtatgctatt ... tgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttattatggctgttccatatttgccattctgacattacttatttgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT
                            ttctgac  putative branch site (score: 2)
                                       cttattt  putative PPT
                                   attacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatagaagttgtactactatcctttaccattatgcttgtattctgcttattatggctgttccatatttgccattctgacattacttatttgtgccccagCCAAACTTGTACCTGTTGGGTACGGTATCAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT

- - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattct