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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatctgaaaattgttgtttgcattacatgttacctttatgataattctgttacacattgtaacatcatgaatagttgatggtaagtcaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAAT

Basic information

species Glycine max
transcript GLYMA05G29410.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G29410.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 2
caatctgaaaattgttgt--ttgcattacatgttacctttatgataattctgttacacattgtaacatcatgaatagttgatggtaagtcaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAAT
||   |||    |  |    | |||    |    | |    | ||  | |  |||||  |  ||  || ||  | |  | |   ||| |  | | ||| ||||| | |||||||||||| || |||||||||||||| |||||  | || ||||| |||||| |||| || ||| ||||||||||||| |||||||| ||||
cagaatgatgcatagtaaagtagcacattagtaaaacacggtcatgttgcatttacatttgttagtatgatacacaaattaacataatttcacc-gtt-cagATCTGCTGGGCATTTTCGATTTACTTGGAGGCAGTGGCAATTCTCCCTCAGTTAGTTTTGCTGCAGAGAAGTAGAAATGTGGACAACTTGACTGGACAAT

upper sequence: GLYMA05G29410.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 2
---caatctgaaaattgttgtttgcattac-atgttacctttatgataattctgttacacattgtaacatcatgaatagttgatggtaagtcaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAAT
   || |||  || |  ||  |||||  |   ||    || | || | ||      |  ||||||  ||  |||  || ||    | |   ||| |  || ||| | |||||||| ||||| || ||||| ||||||||||| ||  | |||||||||||| || | ||||| ||||| ||||| |||||||||||||||||||
cttcactctttaagtattt--ttgcagcattgtggcctctctgtgttgatagccagaatcattgtg-caatatgt-taattctgtgcattccaaaccatttcagGTGTTCTGGGCGTTTTCTATCTACTTAGAGGCAGTTGCTATCCTTCCCCAGTTGGTTCTGCTACAAAGAAGTGGGAATGTCGACAATTTGACTGGGCAAT

upper sequence: GLYMA05G29410.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 2
caatctgaaaattgtt-gtttgcattacatgttacctttatgat-aattct--gttacaca-ttgtaacatcatgaatagttgatggtaa-gtcaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAAT
        |  ||||| | | | |||| | |||   ||| || | ||||||   |   | | |||  |  |     |  | |  || ||| ||  |||| || ||||| |||||||||||||||||||| |||||||| ||||| ||  | |||||||| |||||| | ||| | ||||||||||||||||||||||| |||||||
-----aatatcttgtttgctagtattata-gttgtttttttgcttaattcttaatcttatagttgctatttggcctactgctattgttaatgtatatctattgcagATCTTCTGGGCATTTTCAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAAT

upper sequence: GLYMA05G29410.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S258_82V6.1 (Physcomitrella patens), 3'ss of exon 3
caatctgaaaatt-gttgtttgcattacatgttacctttatgataat---tctgttacacattgtaacatcatgaatagttgatggtaagtcaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAAT-
   | |   | |    |  |    || | | | | | |||| ||| |   |||||| | || | |||     |||||   | ||  |  || ||  ||  |||| |||| ||| | || ||  | || |||||||| ||||| ||| |||| ||||||||||| ||||||||||   ||||||| |||||||| ||  |||||  
tggtttaggattccactactcctgtttc-tttcatccttataatagtgactctgtt-cccagtctaatgg-gtgaatgtctcattttt-gttaacgtggaacagGTTTTGTGGACCTTCTCTCTGTATTTGGAGGCGGTTGCCATAATACCACAGTTGGTTTTATTGCAAAGGACAAGAAATGTAGACAATTTAAC-AGGCAACT

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|151405068|gb|EV274882.1|EV274882
EST:     GGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAG                         ATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
genomic: GGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAGgtcccttgct ... tctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
EST: gi|192294404|gb|FG987333.1|FG987333
EST:     CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAG                         ATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
genomic: CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAGgtcccttgct ... tctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
EST: gi|16343489|gb|BI969084.1|BI969084
EST:     CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAG                         ATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
genomic: CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAGgtcccttgct ... tctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
EST: gi|22933449|gb|BU550588.1|BU550588
EST:     CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAG                         ATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
genomic: CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAGgtcccttgct ... tctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
EST: gi|6726058|gb|AW310457.1|AW310457
EST:     CAAGCTGTGCTATGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAG                         ATCTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
genomic: CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAGgtcccttgct ... tctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
EST: gi|6502251|gb|AW203624.1|AW203624
EST:     CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTACACTGTTCAAGAG                         ATTATCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
genomic: CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAGgtcccttgct ... tctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG
EST: gi|192300473|gb|FG991485.1|FG991485
EST:     CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAG                         ATTTTCTGGGCATTTTCAATATACTTGGAGACAGTTGCAATATTACCCCAG
genomic: CAAGCTTTGCTTTGGCACTCATCTTGCATGAAAAGTTCACTGTTCAAGAGgtcccttgct ... tctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttacacattgtaacatcatgaatagttgatggtaagtcaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAAT
           attgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatctgaaaattgttgtttgcattacatgttacctttatgataattctgttacacattgtaacatcatgaatagttgatggtaagtcaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - tgttgtt
- - - - - - - - - - gcattac
- - - - - - - - - - - - - - tgttacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatg