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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagaattgtatgcgattgtgagtggttttatagagtgataaatgaagttgcagtctgataatatcttatggctttgtttttgatgacaatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT

Basic information

species Glycine max
transcript GLYMA18G47420.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G159388_T01 (Zea mays), 3'ss of exon 1
---ggagaattgtatgcgattgtgagtggttttatagagtgataaatgaagttgcagtctgataatat-cttatggctttgtttttgatgacaatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT
    || ||   |   |||| || |   |  || | |||   ||||| |  ||   |||||  | | | |  |      |  ||    |  |  ||||||| ||||||||||||||| ||||||||||||||||| || ||||||||  | ||||| || ||||| ||  | ||| |  | ||||| |||||||  || || ||
gattgataaacttgatcgat-gtaatgagaattgt-gagacctaaat-accttatcgtctgtcattgtacccacaatactcattaccgtt-ctctattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTGGTGGTGCCACAGCAATCTGGATCTTATTTGAATTGCTTGGCTACCATCT

upper sequence: GLYMA18G47420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G359018_T03 (Zea mays), 3'ss of exon 1
ggagaattgtatgcgattgtgagtggttttatagagtgataaatgaagttgcagtctgataatatctta--tggctttgtttttgatga-caatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT
   || |||  ||   |  ||     | | | | | ||| |  | ||       ||   |   || |||  |  |||  |  ||  |   |  |||||||||||||||||||||||  |||||||||||| ||| || || || ||  | ||||| |||||||| ||  | ||| | || ||||| |||||||  || || ||
---gacttgattggtgtaatgtcaattgtgagacactgagacctaaatacctgatcgtctgtcattttacctaccttactcattactcttctctattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTGGTGGAGCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCT

upper sequence: GLYMA18G47420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G359018_T02 (Zea mays), 3'ss of exon 1
ggagaattgtatgcgattgtgagtggttttatagagtgataaatgaagttgcagtctgataatatcttatggctttgtttttgatgacaatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT---------------------------------------------------------
                                                  |   | | |   || ||||   | ||  | ||     |  |||||||||||||||||||||||  |||||||||||| ||| || || || ||  | ||||| |||||||| ||  | ||| | || ||||| |||||||  || || ||                                                         
--------------------------------------------------gtcattttacc-taccttact-cattactctt-----ctctattttgcagctgctgatgtgttcctgtggaggaacaggaacatctccgccggagtacttggtggagCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTC

upper sequence: GLYMA18G47420.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G46170.2 (Arabidopsis thaliana), 3'ss of exon 1
--ggagaattgtatgcgattgtgagtggttttatagagtgataaatgaagttgcagtctgataatatcttatggctttgtttttgatgacaatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT
  | |  | || |    ||||    |  |  | ||   || ||        ||   |||||     ||| ||   | ||||| | |  |  |   |||||||||||||||||||| ||||||||| | || ||| | || | ||   | ||||| |  || |||||| |||||||||| || ||| || ||||||||||  |
ttgtatgaatgcaataaattggctttattggtttattatgttattgacttctgagttctgagggattctgatttttctgtttctca--atgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT

upper sequence: GLYMA18G47420.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g01760.t01 (Vitis vinifera), 3'ss of exon 1
ggagaattgtatgcgat-tgtgagtggttttatagagt--gataaatgaagttgcagtctgataatatcttatggctttgtttttgatgacaatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT
      || | |   || | |||| | |||  | |     | |   | | |    |   | ||  | |     || ||||||  || ||   || |  |||||  |||||||| || ||||||||||||||||| || ||||| ||  | |||||||||||||||||  | ||||| ||||| || |||||||| || || ||
--ttttttttttaatatatttgagggatttgtttgttccgggtctctcatgccctaactttatcctcttcgtggggtttgttgctg-tgttcatttaatgcagACGCTGATGTATTTTTGTGGAGGAACAAGAAGATCTCTGCCGGAGTACTTGGCGGAGCCACTGCCATGTGGGTGCTTTTCGAATTGCTTGAATACCATCT

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|298179899|gb|HO025114.1|HO025114
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|17963423|gb|BM270172.1|BM270172
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|208315190|gb|GE112664.1|GE112664
EST:     CTCTTCGGAAGGGTAGAGACTCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CTCTTCGGAAGGG-AGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|298176130|gb|HO015535.1|HO015535
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|207826282|gb|GD799421.1|GD799421
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|298177074|gb|HO023435.1|HO023435
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|23057429|gb|BU578103.1|BU578103
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|298169425|gb|HO020785.1|HO020785
EST:     CGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|7926301|gb|AW832327.1|AW832327
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|11687897|gb|BF595573.1|BF595573
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
EST: gi|298180408|gb|HO021961.1|HO021961
EST:     CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAAC                         CTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG
genomic: CCTCTTCGGAAGGGAGAGACCCGTTCACTCCGTTTTCGGCGCCGGAAAACgtaaaacttt ... tattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttgcagtctgataatatcttatggctttgtttttgatgacaatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT
                                 ttttgat  putative branch site (score: 4)
           tgataatatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggagaattgtatgcgattgtgagtggttttatagagtgataaatgaagttgcagtctgataatatcttatggctttgtttttgatgacaatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -tgtatgc
- - - - - - - gattgtg
- - - - - - - - - - -agtggtt
- - - - - - - - - - - - - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - -tgcagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttatgg