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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaattagtggctaatggtgaactgatattaatttcttaaatgactcttgatgggaaactgcatccttctttaaaacaaaattgtaatcatttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCAATCCCCAGCACTGATGATTCCCATTCGGTGCAAATTATTTTACCACAGA

Basic information

species Glycine max
transcript GLYMA08G13300.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13300.3 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 9
aaaaattagtggctaatg-gtgaactgatattaatttcttaaatgactcttgatgggaaactgcatccttctttaaaacaaaattgtaatcatttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCAATCCCCAGCACTGATGATTCCCATTCGGTGCAAATTATTTTACCACAGA
  ||  |    |||  || ||    |        | | || ||  |||           |  |  |  | ||  | || |   |  || | ||| || ||||||||||||||||| |||||||| ||||||||   ||| ||||| ||||||||||| | |||   |||||| || || || ||  ||||||| || || |
-taagatgcaagcttctgtgtttcttccctcctttctttttaaaaactaacataaaatcagagtgtgatgctaaagaagattttgttactaattgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCAATCCCAAACACCAGTGATTCTCACTCAGTTCAGGTTATTTTGCCGCAAA
















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|193684842|gb|FK624760.1|FK624760
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|6567090|gb|AW234717.1|AW234717
EST:     TGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: TGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|10843935|gb|BF067288.1|BF067288
EST:     TATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: TATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|8404346|gb|BE059980.1|BE059980
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|193688874|gb|FK627851.1|FK627851
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|208035181|gb|GD836407.1|GD836407
EST:     CTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|26048272|gb|CA784798.1|CA784798
EST:     CTGCAAAGTGC-AAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|192326977|gb|FK019239.1|FK019239
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|4283991|gb|AI440725.1|AI440725
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCCGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|16105598|gb|BI893338.1|BI893338
EST:     ATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: ATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|26268738|gb|CA819801.1|CA819801
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|192327651|gb|FK020670.1|FK020670
EST:     AAAGTGCAAAAAAGTTGTTTGTGATCTATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: AAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|58015032|gb|CX701774.1|CX701774
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|15203704|gb|BI426472.1|BI426472
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|58016818|gb|CX703560.1|CX703560
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|22521741|gb|BU080552.1|BU080552
EST:     CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
EST: gi|208038580|gb|GD833290.1|GD833290
EST:     CAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAG                         GTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA
genomic: CAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaa ... atttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgatgggaaactgcatccttctttaaaacaaaattgtaatcatttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCAATCCCCAGCACTGATGATTCCCATTCGGTGCAAATTATTTTACCACAGA
 tcttgat  putative branch site (score: 4)
                                           tcatttc  putative PPT
                      ttctttaaaacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaattagtggctaatggtgaactgatattaatttcttaaatgactcttgatgggaaactgcatccttctttaaaacaaaattgtaatcatttcaacagGTGAGGAAGGTTGGTAGGGTTGCAAGAGCAATAGCCATAATGAGTCACCCAATCCCCAGCACTGATGATTCCCATTCGGTGCAAATTATTTTACCACAGA

- - - - gtggcta
- - - - - - - - - - - - - - - - - - - - - - - -cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa