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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatactcttctcaacattaatgttgtacaacatctcttgttggttaccacatacttttctttgatatccctgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAACAGTCACTGAAAGGATACGAG

Basic information

species Glycine max
transcript GLYMA01G07070.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 2
ttatactcttctcaacattaatgt-tgtacaacatctcttgttggttaccacatacttttctttgatatccctgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAACAGTCACTGAAAGGATACGAG------------
  |  || | |   | ||| |  | ||||||        |     ||   |     ||||   |  ||||  |  |    |||     |   |  || |||||||||||| || |  |||||||| |||||||||||||||||||| ||||||||||||||  |||| ||||||||||| || ||||||            
ggaggctgtgcaatatatttacatatgtacatttgaaactaaacttttatatggggttttaagtt-tatctttcctggtgttttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT
















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|192300602|gb|FG988899.1|FG988899
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|7590427|gb|AW706180.1|AW706180
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|37996365|gb|CF807954.1|CF807954
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|58019744|gb|CX706486.1|CX706486
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|58019157|gb|CX705899.1|CX705899
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|58019309|gb|CX706051.1|CX706051
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|58022129|gb|CX708870.1|CX708870
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|192302132|gb|FG995812.1|FG995812
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|18735497|gb|BM528797.1|BM528797
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|58018950|gb|CX705692.1|CX705692
EST:     TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGCATCAGCAGAAGCTAGTGTTTTCTACTATAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccacatacttttctttgatatccctgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAACAGTCACTGAAAGGATACGAG
                                            ttttgat  putative branch site (score: 4)
                    tatccctgatttcctt  CT-rich tract
                                  tttattcttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatactcttctcaacattaatgttgtacaacatctcttgttggttaccacatacttttctttgatatccctgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAACAGTCACTGAAAGGATACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - ctcaaca
- - - - - - - - - - -tgttgta
- - - - - - - - - - - - - - caacatc
- - - - - - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - cacatac