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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgcaacagctacactgacgacgtttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT

Basic information

species Glycine max
transcript GLYMA01G03260.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 7
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgcaacagctacactgac--gacgtttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT
   |     ||||||| | ||  |   || | |      |   |    | | |    |    |  |  |   | |   |    |||| ||||  | |  |||||||| || |||||||||||||||||||||||  |||| |||||||||||||| |  || || |||
--tcatgtaatgtaagattttactttgaagtttggatagtagcacagataccatttttctgtttgcttgtgatctaattacgttcctcatttcatatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT

upper sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgcaacagctacactga----cgacgtttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT
     ||| ||   |      ||     | |||||  |  |  ||   || |     |    | |     |||| |   | ||  | |  ||||    ||||||||||| |||||||||||||||||||||||||||  ||| ||||| |||||||| |  ||||| |||
---tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttc-aatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
















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|208191199|gb|GD989187.1|GD989187
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCAT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCAT
EST: gi|120491744|gb|EH219911.1|EH219911
EST:     AATGTGTACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|209697563|gb|BW660570.1|BW660570
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|10233337|gb|BE802225.1|BE802225
EST:     AATGTGGACAGCTAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTACTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|14205591|gb|BG839269.1|BG839269
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|19347413|gb|BM892293.1|BM892293
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|15815783|gb|BI788058.1|BI788058
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|14205453|gb|BG839131.1|BG839131
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCRCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|20498717|gb|BQ273647.1|BQ273647
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAG
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAG
EST: gi|19348485|gb|BM893026.1|BM893026
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|9902378|gb|BE611346.1|BE611346
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTAGATGAGATCTACAACGTTGCTTTAATATCACTTAGTCCAAGTGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|17400767|gb|BM177549.1|BM177549
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|51343112|gb|CO983845.1|CO983845
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATNNACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|31471989|gb|CD414017.1|CD414017
EST:     AATGTGGAAAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|31309987|gb|CD395190.1|CD395190
EST:     TTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: TTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|51337166|gb|CO981032.1|CO981032
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|14206264|gb|BG839942.1|BG839942
EST:     AAATGACCAACATTCCTCCAGAGG                         ACAGTTGATGAGATNTACAAGGGTTGCATCAATATCACTTAGTCCAAATG
genomic: AAATGACCAACATTCCTCCAGA-Ggtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAA-GGTTGCATCAATATCACTTAGTCCAAATG
EST: gi|31464694|gb|CD406707.1|CD406707
EST:     TTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: TTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|7234812|gb|AW570145.1|AW570145
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|7234825|gb|AW570158.1|AW570158
EST:     GAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: GAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|31561480|gb|CD487318.1|CD487318
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|22932146|gb|BU549285.1|BU549285
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCANCATTNNTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|14205407|gb|BG839085.1|BG839085
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|120529211|gb|EH257345.1|EH257345
EST:     AATGTGGACAGCGAGGTGGATATTTGGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|7796142|gb|AW781539.1|AW781539
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTTAGTCCCAATGG
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCAC-TTAGTCCAAATGT
EST: gi|120492417|gb|EH220584.1|EH220584
EST:     TGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: TGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|26269528|gb|CA820591.1|CA820591
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|27424258|gb|CA935778.1|CA935778
EST:     CCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: CCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|120532614|gb|EH260747.1|EH260747
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
EST: gi|120491540|gb|EH219707.1|EH219707
EST:     AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAG                         ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT
genomic: AATGTGGACAGCGAGGTGGATATTTTGAAATGACCAACATTCCTCCAGAGgtttgccttt ... tcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcaacagctacactgacgacgtttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT
                       cgtttttcttttatcc  CT-rich tract
                         tttttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgcaacagctacactgacgacgtttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT

- - - - catgtaa
- - - - - - - - - - tcataca
- - - - - - - - - - - - - - - - - -cctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - caacagc