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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCTATGACTGTGGCCATGCATGATGCTCCCATTAAAGAGGTTGCTTGGATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAAgtaaacattcttttctctgtttatagtttttcccatttgaaatgagaatcaaaagtatgacagtaagtttaggtgctacttttgttgcaatattgtacaa...

Basic information

species Vitis vinifera
transcript Vv12s0055g00900.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 4
AACCTATGACTGTGGCCATGCATGATGCTCCCATTAAAGAGGTTGCTTGGATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAAgtaaa----cattcttttctctgtttatagtttttcccatttgaaatgagaatcaaaagtatgacagtaagtttaggtgctacttttgttgcaatattgtacaa
|||| |||||||| |||||||||||||| ||||| |||||  |||||||||| || || |||||||| |||| |||||||||||||||||||||| | ||||||      |   ||| ||   |||| ||   ||    ||| || |     |  | |  || | | ||  |  |     | |  |  |  ||| ||| ||   
AACCAATGACTGTTGCCATGCATGATGCACCCATCAAAGAACTTGCTTGGATTCCTGAAATGAACCTTTTAGTCACAGGAAGCTGGGACAAGACTATGAAgtaatgtgctagcatttgctgcctttacagcaatttgtttttaaattatatctttagaa-attagaatatatgaaaaatatcccgtaatatcaacattata---

upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 4
AACCTATGACTGTGGCCATGCATGATGCTCCCATTAAAGAGGTTGCTTGGATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAAgtaa-acatt----cttttctctgtttatagtttttcccatttgaaatg-agaatcaaaagtatgacagtaagtttaggtgctacttttgttgcaatattgtacaa
|||| |||||||| ||||||||||| || ||||| ||||| ||||||||||| || || |||||||| |||| |||||| ||||||||||||||| | |||||   |  |     ||| ||   |||| ||   ||    ||| || |  |   | | || |  ||   ||||   |     ||  |   |  ||||||| ||   
AACCAATGACTGTTGCCATGCATGACGCACCCATCAAAGAAGTTGCTTGGATTCCTGAAATGAACCTTTTAGTCACAGGGAGCTGGGACAAGACTTTGAAgtactgcgctagcattttgctgcctttacagcaatttgtttttaaattatacctttagaaattagaatataagaaaaa----tatctaaatatcaatattatat--
















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|71856427|gb|DT005482.1|DT005482
EST:     ATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAA                         GTATTGGGATACAAGGCAGCCTAATCCTGTGCATACCCAGCAA
genomic: ATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAAgtaaacattc ... gtattttcagGTATTGGGATACAAGGCAGCCTAATCCTGTGCATACCCAGCAA
EST: gi|30125531|gb|CB910870.1|CB910870
EST:     ATCCCAGAGATGAACCTCTTAGCCACAGGAAGTTGGGACAAGACTCTCAA                         GTATTGGGATACAAGGCAGCCTAATCCTGTGCATACCCAGCAACTCCCTGA
genomic: ATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAAgtaaacattc ... gtattttcagGTATTGGGATACAAGGCAGCCTAATCCTGTGCATACCCAGCAACTCCCTGA
EST: gi|351043163|gb|FQ451336.1|FQ451336
EST:     ATCCTAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAA                         GTATTGGGATACAAGGCAGCCTAATCCTGTGCATACCCAGCAACTCCCTGA
genomic: ATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAAgtaaacattc ... gtattttcagGTATTGGGATACAAGGCAGCCTAATCCTGTGCATACCCAGCAACTCCCTGA
EST: gi|71859699|gb|DT008754.1|DT008754
EST:     ATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAA                         GTATTGGGATACAAGGCAGCCTAATCCTGTGCATACCCAGC
genomic: ATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAAgtaaacattc ... gtattttcagGTATTGGGATACAAGGCAGCCTAATCCTGTGCATACCCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCTATGACTGTGGCCATGCATGATGCTCCCATTAAAGAGGTTGCTTGGATCCCAGAGATGAACCTCTTAGCCACAGGAAGCTGGGACAAGACTCTTAAgtaaacattcttttctctgtttatagtttttcccatttgaaatgagaatcaaaagtatgacagtaagtttaggtgctacttttgttgcaatattgtacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagta