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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttaggattaatttctgttcagaaaggtttcggcaggaccattgtaatcaattttttgttgatgtctctgttttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGTGGTGCCTTTTCATGGGAAATTGCTCCAGTTGAAGTCTCTGGTGGAAGAG

Basic information

species Glycine max
transcript GLYMA14G00760.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------------------------------------------gtattttaggattaatttctgttcagaaaggtttcggcaggaccatt----gtaat-----caattttttgt---tgatgtctctgttttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGTGGTGCCTTTTCATGGGAAATTGCTCCAGTTGAAGTCTCTGGTGGAAGAG
                                                                                      | || ||   ||| |||| |    | ||  |||     |   |   |    ||||      |||||||||||   |  |  ||     ||  || ||||||   ||||| ||||| || ||||| ||||| ||||||||||||||  ||||||||||| |||||||||||| |||                       
gtatcattttgtacccatatattgtgttgcaaacaatttcacaagaaaccttacacttcaacttccagtagttcctccctattcatgcatattgcaattcatttgtaaaaataatcgttatcttaaatctgcttttagtaacacctacaattttttgtgacttgttcctgcacatttgccacagGATGCTTATGCTATTCATAGCTTTGAGCGTGGTATTGCTGCCCAAGATGGTGGTGCCTTTGCATGGGAAATTGTTCCG----------------------
















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|19052939|gb|BM731606.1|BM731606
EST:     TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAG                         GATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
genomic: TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAGgtattttagg ... ttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
EST: gi|192312109|gb|FK003872.1|FK003872
EST:     TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAG                         GATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
genomic: TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAGgtattttagg ... ttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
EST: gi|192328380|gb|FK020091.1|FK020091
EST:     TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAG                         GATAACTATGCAATTCAGAGTTTTGAACATGGAATTGCTGCCCAAGAAAGT
genomic: TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAGgtattttagg ... ttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
EST: gi|193670964|gb|FK613800.1|FK613800
EST:     TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAG                         GATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAA
genomic: TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAGgtattttagg ... ttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAA
EST: gi|192317815|gb|FK009407.1|FK009407
EST:     TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAG                         GATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
genomic: TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAGgtattttagg ... ttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
EST: gi|192312110|gb|FK003873.1|FK003873
EST:     TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAG                         GATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
genomic: TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAGgtattttagg ... ttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
EST: gi|192329988|gb|FK021574.1|FK021574
EST:     TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAG                         GATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
genomic: TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAGgtattttagg ... ttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
EST: gi|37994372|gb|CF806118.1|CF806118
EST:     TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAG                         GATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT
genomic: TGTGTGCTGAGCTATGTGCAGATAACCATGCATTAACAAGAGACGACCAGgtattttagg ... ttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcggcaggaccattgtaatcaattttttgttgatgtctctgttttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGTGGTGCCTTTTCATGGGAAATTGCTCCAGTTGAAGTCTCTGGTGGAAGAG
                             tgttgat  putative branch site (score: 4)
                                   tgtctctgttttcccc  CT-rich tract
             attgtaatcaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttaggattaatttctgttcagaaaggtttcggcaggaccattgtaatcaattttttgttgatgtctctgttttcccctcagGATAACTATGCAATTCAGAGTTTTGAACGTGGAATTGCTGCCCAAGAAAGTGGTGCCTTTTCATGGGAAATTGCTCCAGTTGAAGTCTCTGGTGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA