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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtaatcagctagtagcttttcttctctatagatttgtattatctatgcgatatgaaatttgagatagttacaagttataacactgttctgtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGTTCAGGATGGAGCTGTTCCTGCTTATCTCCTTGATCGTGATAACACGACC

Basic information

species Glycine max
transcript GLYMA10G00490.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------ggtaatcagctagtagcttttcttctctat-agatttgtattatctatgcgatatgaaatt-tgagatagttacaa-gttataacactgttctgtgtca--acagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGTTCAGGATGGAGCTGTTCCTGCTTATCTCCTTGATCGTGATAACACGACC
                                       || |  || |  ||  |  | |  |  ||  ||| |   | |  ||   | | ||   || |||||   |||||  | | | |   |  | | |||||  |||| |||   ||||||||||| ||| | || ||||| ||| ||||||| ||||||||||| |||||||||||||||||||| |||||||||||  |||| || 
gtaagtgtttcgtcgtattctctgagaatctatcattaagtgaa-agatgttaagtagtataattgattggatattcctaagttaataggtgtggttttatgagaatcttacattggtttgatttttatttttgtcataacagATTGAAAATGCATGAAGAGTCATCATCAAGGCGTAAGGCTGATGAGAATGTTCAGGAAGGAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACT

upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 3
ggtaatcagcta-gtagcttttcttctctatagatttgtattatctatgcgatatgaaatttgagatagttacaagttataacactgttctgtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGTTCAGGATGGAGCTGTTCCTGCTTATCTCCTTGATCGTGATAACACGACC
  |  |    ||  |    | |  |   ||||||||  |  |||           || | |    |  | |     || | |          | |  |||| ||||||||||||||||||||| | ||||||||||||   |||||| ||||||| || || ||||||||||| ||||| || |||||||| |  || || 
-atgttatattacatcatgtgtggtagttatagattgatggtatgcccattgatggataatgattactgatgttgtttgttaattatcatcattttgacagATTGGCTATGCATGAAGAATCATCATCTAGGCGCAAGGTGGATGATGATGTTCATGAAGGGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACA
















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|26059399|gb|CA802313.1|CA802313
EST:     AAATGATTGCCAAGAAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAATGATTGCCAAG-AAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|11413156|gb|BF425167.1|BF425167
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|17400258|gb|BM177032.1|BM177032
EST:     ATTATGCTGAAAAGGCACAGATGAAGAAGAC                         AAAGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: ATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|20498024|gb|BQ272954.1|BQ272954
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|15813104|gb|BI785379.1|BI785379
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|298179957|gb|HO025172.1|HO025172
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|5606189|gb|AI900287.1|AI900287
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|298178157|gb|HO027540.1|HO027540
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|209725840|gb|BW654703.1|BW654703
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|120530814|gb|EH258947.1|EH258947
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|298182139|gb|HO026314.1|HO026314
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTACGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|298189817|gb|HO038220.1|HO038220
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|192329667|gb|FK022933.1|FK022933
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|192333080|gb|FK026409.1|FK026409
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
EST: gi|120530581|gb|EH258714.1|EH258714
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgatatgaaatttgagatagttacaagttataacactgttctgtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGTTCAGGATGGAGCTGTTCCTGCTTATCTCCTTGATCGTGATAACACGACC
                              ttataac  putative branch site (score: 2)
     atatgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaatcagctagtagcttttcttctctatagatttgtattatctatgcgatatgaaatttgagatagttacaagttataacactgttctgtgtcaacagTTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGTTCAGGATGGAGCTGTTCCTGCTTATCTCCTTGATCGTGATAACACGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - tctatgc