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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatcacgattcaatacccattagaggctaaaatagattaagatctatatggtggctaactggttaagttgctgtttgctgaatttgttatgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAAGAACATTGAGATATGGAAGATCAAGAAATTGATCAAGGCTCTGGAAGCT

Basic information

species Glycine max
transcript GLYMA02G07560.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07560.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g12240.t01 (Vitis vinifera), 3'ss of exon 2
tcaatcacgattcaatacccattagaggctaaaatagattaagatctatatggtggctaactggttaagttgctg---tttgctgaatttgttatgttt----------atagGCTAGTCTTC----CTATTATCACAA--ACAATGTCTGACAGTCAAGAATCTGACAAGAACATTGAGATATGGAAGATCAAGAAATTGATCAAGGCTCTGGAAGCT
    ||| |  |   |    |   ||  ||  |     |||   |   | |      |   |  | ||  | |     ||| |  | ||| || | | |          ||  | |||  | |     || || |  |   |||||| | ||  |||| ||| | || |||||||||||||||||||||||||| || |||||||              
----tcatgcctttttttttaaaggaatctgcacctt-ttagttttcttttctcctgtgcataatcaaactcccagaattttcaaagtttattttttctttgcagGTAAATCAGTTAGCTTCCACAGTTAGTACCGTACTTACAATGGCAGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAAAAGTTGATCA--------------

upper sequence: GLYMA02G07560.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0041g00730.t01 (Vitis vinifera), 3'ss of exon 1
-----tca-atcacgat-tcaatacccattagaggctaaaatagattaagatctatatggtgg-ctaactggttaagttgctgtt-tgctgaatttgttatgtttatagGCTAGTCTTCC-------TATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAAGAACATTGAGATATGGAAGATCAAGAAATTGATCAAGGCTCTGGAAGCT
     ||| |||| ||| | ||   |||||    | |  | |   | |  ||  |  |  | |  | |    || ||||  | || |||    ||||       | |    || | | |        || |||     |||||| ||||  |||| ||| | || ||||||||||||||||||||||||||||| |||||                
tcacctcatatcaggatattaagcaccatttttagttttattttttcattatggaactactagattcagaatttgagtttatattctgccatctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAGAAGTTGAT----------------
















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|208336682|gb|GE135982.1|GE135982
EST:     CTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: CTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|19936594|gb|BQ080934.1|BQ080934
EST:     GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|11413690|gb|BF425701.1|BF425701
EST:     CAGTTACACCCCTCTTTTCTC-TCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: CAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|209727715|gb|BW658452.1|BW658452
EST:     TTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTNCTGACAGTCAAGAATCTGACA
genomic: TTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGT-CTGACAGTCAAGAATCTGACA
EST: gi|7284163|gb|AW596761.1|AW596761
EST:     GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|151398672|gb|EV268543.1|EV268543
EST:     GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|4305777|gb|AI443810.1|AI443810
EST:     GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|298170860|gb|HO015836.1|HO015836
EST:     GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGCCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|213595933|gb|DB966264.1|DB966264
EST:     GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|193579848|gb|FK534965.1|FK534965
EST:     GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|19937184|gb|BQ081186.1|BQ081186
EST:     GTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|209712909|gb|BW679188.1|BW679188
EST:     TTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: TTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|208125477|gb|GD922887.1|GD922887
EST:     GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|207702100|gb|GD681973.1|GD681973
EST:     GTTTCAGTTTCGCCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGCCAAGAATCTGACAA
genomic: GTTTCAGTTTCACCCCTCTTTTCTCATCTCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
EST: gi|19937215|gb|BQ081201.1|BQ081201
EST:     TCTAACATCATAGTCCTCAGAG                         GCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA
genomic: TCTAACATCATAGTCCTCAGAGgtacggtccc ... atgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatatggtggctaactggttaagttgctgtttgctgaatttgttatgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAAGAACATTGAGATATGGAAGATCAAGAAATTGATCAAGGCTCTGGAAGCT
         ggctaac  putative branch site (score: 2)
                                     aatttgttatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatcacgattcaatacccattagaggctaaaatagattaagatctatatggtggctaactggttaagttgctgtttgctgaatttgttatgtttatagGCTAGTCTTCCTATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAAGAACATTGAGATATGGAAGATCAAGAAATTGATCAAGGCTCTGGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
-caatcac
- - - - - - caatacc
- - - - - - - - - - - - - - - - - - - - - - - - -atggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa