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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaattagtggtgaatggtgaactgatattaatttcttaaatgactcttgatgggaaattgcgtccttctttaatacaaaattgtaatcatttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCAATCCCCAGCACTGATGATTCCCATTCAGTGCAAATTATTTTACCACAGA

Basic information

species Glycine max
transcript GLYMA05G30140.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30140.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 9
-aaaaattagtggtgaatggtgaactgatattaatttcttaaatgactcttgatgggaaattgcgtccttctttaatacaaaattgtaatcatttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCAATCCCCAGCACTGATGATTCCCATTCAGTGCAAATTATTTTACCACAGA
 || |   |    |   || |       |  |   || |||||  |||           |  | ||  | ||  |  | |   |  || | ||| || ||||||||||||||||| |||||||| || || ||   ||| ||||||||||||||||| | |||   |||||| || ||||| ||  ||||||| || || |
taagatgcaagcttctgtgtttcttccctcctttctttttaaa-aactaacataaaatcagagtgtgatgctaaagaagattttgttactaattgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCAATCCCAAACACCAGTGATTCTCACTCAGTTCAGGTTATTTTGCCGCAAA
















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|192322507|gb|FK014628.1|FK014628
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|192313375|gb|FK005147.1|FK005147
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|208295615|gb|GE091738.1|GE091738
EST:     TGAC-AAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: TG-CAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|207827157|gb|GD798294.1|GD798294
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAACCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|192313374|gb|FK005146.1|FK005146
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAAGTTGG
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGG
EST: gi|193656048|gb|FK606678.1|FK606678
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCA
EST: gi|14989997|gb|BI315670.1|BI315670
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|207712773|gb|GD693397.1|GD693397
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGCAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|207819023|gb|GD790399.1|GD790399
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|7233927|gb|AW569269.1|AW569269
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATTCATCATATTTGCCTGTCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|6915949|gb|AW397479.1|AW397479
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTANGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|4291506|gb|AI437629.1|AI437629
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|208156728|gb|GD957262.1|GD957262
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|24205309|gb|BU964562.1|BU964562
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|14125915|gb|BG790353.1|BG790353
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
EST: gi|120533574|gb|EH261707.1|EH261707
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCCGATAGCCATCATGAGCCACCC
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGC-GATAGCCATCATGAGCCACCC
EST: gi|208226200|gb|GE025527.1|GE025527
EST:     CTGCAAAGTGT-AAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA
genomic: CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgatgggaaattgcgtccttctttaatacaaaattgtaatcatttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCAATCCCCAGCACTGATGATTCCCATTCAGTGCAAATTATTTTACCACAGA
                        ctttaat  putative branch site (score: 4)
                                           tcatttc  putative PPT
                      ttctttaatacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaattagtggtgaatggtgaactgatattaatttcttaaatgactcttgatgggaaattgcgtccttctttaatacaaaattgtaatcatttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGGGCGATAGCCATCATGAGCCACCCAATCCCCAGCACTGATGATTCCCATTCAGTGCAAATTATTTTACCACAGA

- - - -agtggtg
- - - - - - - aatggtg
- - - - - - - - - - - - - - - - - - - - - - - -cttgatg