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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaatgtagttatggtgattgagttggaaaattagcagattttgttagttcctcttcattctgtcttattgacccggtaagtcccatttatttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC

Basic information

species Glycine max
transcript GLYMA09G36860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36860.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g65560.1 (Oryza sativa), 3'ss of exon 3
-gaaaatgtagttatggtgattgagttggaaaattagcagattttgttagttcctcttcattc-tgtcttattgacccgg--taagtcccatttatttctct-agATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC
   ||  || |  ||| |    |  ||   | | || ||   ||   ||||||   || |||    | |  | || | |   ||  |   || ||||||| | |||| |  || ||| | ||||| ||| |||| |  || || ||| | |||||||||||||| |||||||| |||||||||||||||||  |||||||| | |
tcgaagcgttgaaatgctag--gctttaacatactaaca---ttacatagttctgtttaattaacatatggtagaactgacctatttgggatatatttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC

upper sequence: GLYMA09G36860.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G005061_T03 (Zea mays), 3'ss of exon 1
gaaaatgtagttatggtgattgagttggaaaattagcagattttgttagttcctcttcattctgtcttattgacccggtaagtcccatttatt-tctcta---gATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC
     | |   |   ||  ||  |||  | |  ||  | ||  |   |  |    |  ||  ||| ||    |     |  |  |  | | || ||||||   ||| | ||| ||  | ||||| |||||||| || || || ||||| ||||| |||||  |||||||||||||||| |||||||||||| | ||||||||||
----ttctgagtgcagtagttttgtttaacatataatatatgatcagaactaacataaatagtgtattgacaatgttatctgctctctctgttctctctatcagATCTATAGAGAGGCTACTGGAACTGCTTCTGTTGATGATACAAGCTATGGTGATCCCATACAGAAGGCAGAAGCTATGGCTTTTCGTCGTGCTTGTGCAC

upper sequence: GLYMA09G36860.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G120814_T03 (Zea mays), 3'ss of exon 3
gaaaatgtagtta--tggtgattgagttggaaaattagcagattttgttagttcctcttcattctgtcttattgacccggtaagtcccatttatttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC
|| ||| |   |   | ||  ||  ||   | |  ||  | ||      |  |     |   |      | |||  || |      |  |||  |     |||| | ||| ||  | ||||| |||||||| || || || ||||  ||||| ||||| ||||||||||||||| | |||||||||||| | |||||||| |
gacaatttctctgcctagtagttttgtctaacatataatatatgaccaaaactaacagtgtattgacaatgttg--cctgctctctctgttttctctatcagATCTATAGAGAGGCCACTGGAACTGCTTCTGTTGATGATACAATCTATGGTGATCCCGTACAGAAGGCAGAATCTATGGCTTTTCGTCGCGCTTGTGCGC

upper sequence: GLYMA09G36860.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G71310.1 (Arabidopsis thaliana), 3'ss of exon 3
-gaaaatgtagttatggtgattgagttggaaaattagcagattttgttagttcctcttcattctgtcttattgacc--cggtaagtcccatttatttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC
        || || |  |||     ||      | |     ||||| | ||  ||  |         | |||  |      | | |    |    || || ||||||||||||||||||| |||||  | || ||||| |||| | | ||||| ||| |||| || ||||| ||||||||||| |||||  | || |||||| 
tccttgcatactt-tcttgagcatattatgttttcattg--ttttgcttgtaacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA

upper sequence: GLYMA09G36860.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0089g00930.t01 (Vitis vinifera), 3'ss of exon 3
gaaaatgtagtta--tggtgattgagttggaaaattagcagattttgttagttcctcttcattctgtctt-attgacccggtaagtcccatttatttct-ctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC
    ||  || ||  | ||  || |  |  ||||| |  |||                  |  ||  ||| | |  ||||  |  |    | | ||||  | |||| |  || || ||||| || ||||||| |||||| |||||| | ||||||||||||||||||||||| ||||||||||||||  |  | ||||||||||
---cat-cagctactttgttttttatctcaaaaatgaaaagaggccaaacccctgaaggaaaactaacttgaattgcccgtaacattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC

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|298192938|gb|HO033372.1|HO033372
EST:     AGTCTGTCTCCGTTGTCTACCGAGTTACCCTTTATGGGACTGATGCTGAG                         ATATTTAGGGAATCAACTGGTACTGCTTCAGTAGAAGACACAAGTTATGGA
genomic: AGTCTGTCTCCGTTGTCTACCGAGTTACCCTTTATGGGACTGATGCTGAGgtacgtgcaa ... atttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGA
EST: gi|298177394|gb|HO027175.1|HO027175
EST:     AGTCTGTCTCCGTTGTCTACCGAGTTACCCTTTATGGGACTGATGCTGAG                         ATATTTAGGGAATCAACTGGTACTGCTTCAGTAGAAGACACAAGTTATGGA
genomic: AGTCTGTCTCCGTTGTCTACCGAGTTACCCTTTATGGGACTGATGCTGAGgtacgtgcaa ... atttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGA
EST: gi|10231996|gb|BE800884.1|BE800884
EST:     AGTCTGTCTCCGTTGTCTACCGAGTTACCCTTTATGGGACTGATGCTGAG                         ATATTTAGGGAATCAACTGGTACTGCTTCAGTAGAAGACACAAGTTATGGA
genomic: AGTCTGTCTCCGTTGTCTACCGAGTTACCCTTTATGGGACTGATGCTGAGgtacgtgcaa ... atttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttcctcttcattctgtcttattgacccggtaagtcccatttatttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC
                      tattgac  putative branch site (score: 2)
                                     tcccatttatttctct  putative PPT
                                         atttatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaatgtagttatggtgattgagttggaaaattagcagattttgttagttcctcttcattctgtcttattgacccggtaagtcccatttatttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- -aatgtag
- - - - - -tatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtccca