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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcattttgtttgagaatcggagattttaatcatctatctctcgaagctaactgcaagaaagttgacaatttgacatatgtatcatacttttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTGAACCAGTATCCACAGTCAAAGGTGGAGATAAGCCTCTTTCACCACCAAA

Basic information

species Glycine max
transcript GLYMA09G36770.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 3'ss of exon 6
--tgcattttgtttgagaatcggagattttaatcatctatctctcgaagctaactgcaagaaagttgacaatttgacatatgtatcatacttttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTGAACCAGTATCCACAGTCAAAGGTGGAGATAAGCCTCTTTCACCACCAAA
  |   |||   || | ||| |  || ||| || ||  |      |    |     ||    |  |  | |  |      |  |||      ||| |  ||||||| ||||||||||| ||||||||||||||||||||||||||||| ||||||||||| || ||||| ||  |||||  | ||||||| ||||| || ||
aatagttttcagtt-aaaattgatgaatttgataatggagaaaaggggattccactcattgtatatacctaccttcatggtaaatctgttgattgata-cagGATACCTTGCATGTGCCCGCTGTTCAAGCACAGGAGCACTTGTTCTTATTGAACCAGTCTCAACAGTGAATAGTGGAAGTCAGCCTCTATCACCGCCTAA

upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0013g00350.t01 (Vitis vinifera), 3'ss of exon 5
------tgcattttgtttgagaatcggagattttaatcatctatctctc-gaagctaactgcaagaaagttgacaatttgacatatgtatcatacttttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTGAACCAGTATCCACAGTCAAAGGTGGAGATAAGCCTCTTTCACCACCAAA
      |   |||   || | ||| |  || ||| || ||        | | ||   ||| ||    | ||  | |  |     || | |       ||| |  ||||||| ||||||||||| |||||||||||| | ||||| |||||||| | |||||| || || |||||||| ||||||    ||||||| ||||| || ||
atctaatagttttcagtt-aaaattgttgaatttgataatgaggaagacaggagtccact-cattgtatttacctacatagttaatctgttga----ttgata-cagGATACCTTGCATGTGCCCGCTGTTCAAGCTCGGGAGCGCTTGTTCTTAGTGAACCTGTCTCAACAGTCAATGGTGGAAGACAGCCTCTATCACCTCCTAA
















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|120490982|gb|EH219149.1|EH219149
EST:     CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
EST: gi|254342696|gb|GR858858.1|GR858858
EST:     CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
EST: gi|6846776|gb|AW349066.1|AW349066
EST:     CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
EST: gi|120490996|gb|EH219163.1|EH219163
EST:     CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
EST: gi|31474915|gb|CD416943.1|CD416943
EST:     CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
EST: gi|254342695|gb|GR858857.1|GR858857
EST:     CAATGTAAAACAGCAG-AGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
EST: gi|31469669|gb|CD411697.1|CD411697
EST:     CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
EST: gi|21285677|gb|BQ473548.1|BQ473548
EST:     CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTG
EST: gi|15336929|gb|BI497585.1|BI497585
EST:     CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTG                         GATATCTTGCATGTGCTCGCTGTTCAAGCACAG
genomic: CAATGTAAAACAGCAGGAGCAGAAAAGATGCAAATACTGTCTTGGCACTGgtaagatttc ... ttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctaactgcaagaaagttgacaatttgacatatgtatcatacttttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTGAACCAGTATCCACAGTCAAAGGTGGAGATAAGCCTCTTTCACCACCAAA
                                          cttttgct  CT-rich tract
                              atatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcattttgtttgagaatcggagattttaatcatctatctctcgaagctaactgcaagaaagttgacaatttgacatatgtatcatacttttgctgtcagGATATCTTGCATGTGCTCGCTGTTCAAGCACAGGAGCACTTGTTCTGATTGAACCAGTATCCACAGTCAAAGGTGGAGATAAGCCTCTTTCACCACCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catatgt