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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctgatgagcatacatttttaaattgaacagaaaattcagaagttagagttatgtttatacaagcatttaatgggtcattgctgatatttttctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG

Basic information

species Glycine max
transcript GLYMA17G01180.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01180.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G17270.1 (Arabidopsis thaliana), 3'ss of exon 8
-------tttctgatgagcatacatttttaaattgaacagaaaattcaga-agttagagttatgtttatacaagcatttaa-tgggtcattgctgatatttttctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG
         | |      ||||   ||  |   | ||        || |  ||  |||||||   ||  | |   | | ||    ||  | |   |   |    ||||||| ||||||||||  || ||||||||||| || ||||||||||||
gtatgatgctttacccgccataacattaaattcttaatttctggctctgccagacagagttaatattggaaacaaactgaaacctgtggtcgaaaactctcaaatgcagGAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAG

upper sequence: GLYMA17G01180.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 8
tttctgatgagcatacatttttaaattgaacagaaaattcagaagttagagttatgtttatacaagcatttaatgggtcattgctgatattttt-ctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG
                        |     |   |   || |   ||    |  || |||||  ||  |||      | |   |      ||    | ||||||||||||||||| || || ||||||||||| ||||| || |||
----------------------gtacgatgctttactctccgtttttttgttcttgattataatag--tttgggaaataaactcaatcgcttgaattacagGAGTCAAGCAAGAGTATCCAAATAGAAGCATTCCATGTCTTTAAG

upper sequence: GLYMA17G01180.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 8
---tttctgatgagcatacatttttaaattgaacagaaaattcagaagttagagttatgtttatacaagcatttaatgggtcattgctgatatttttctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG
    |  |    || ||  |    ||||      || || | |  ||  ||  |  |  |||  ||||   ||| ||   |  | | | || || || | ||||||||||||||||| || ||||| ||||| |||||||||||||||
accatcttcccaagtatgaaggactaaaaattttagtaactgct-aaactaatgagacattttaacaaagctttgataaat-gtggattatcttctttt-cagGAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG

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|16345977|gb|BI971572.1|BI971572
EST:     GATATGTCAGCTNNNGAGACAACTTAAGGATTTTAATGAATCTTCTACGT                         GAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG
genomic: GATATGTCAGCTCACGAGACAACTTAAGGATTTTAATGAATCTTCTACGTgtatggtcct ... ttttctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG
EST: gi|7796054|gb|AW781451.1|AW781451
EST:     GATATGTCAGCTCACGAGACAACTTAATGATTGTAATGAATCTTCTACGT                         GAGTCAAAGCA-GAGCATACAGATAGAAGCATTTCATGCGTTCAAG
genomic: GATATGTCAGCTCACGAGACAACTTAAGGATTTTAATGAATCTTCTACGTgtatggtcct ... ttttctgcagGAGTCAA-GCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG
EST: gi|17400886|gb|BM177668.1|BM177668
EST:     GATATGTCAGCTCACGAGACAACTTAAGGATTTTAATGAATCTTCTACGT                         GAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG
genomic: GATATGTCAGCTCACGAGACAACTTAAGGATTTTAATGAATCTTCTACGTgtatggtcct ... ttttctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagagttatgtttatacaagcatttaatgggtcattgctgatatttttctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG
                                    tgctgat  putative branch site (score: 3)
                                          tatttttct  CT-rich tract
      ttatgtttatacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctgatgagcatacatttttaaattgaacagaaaattcagaagttagagttatgtttatacaagcatttaatgggtcattgctgatatttttctgcagGAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC