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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAATACCCAAAGGGCCCGGAGCCAGCTTCTGGAAAGCCATCTAGCAAAGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattactggtggtgccattttaaataattggtattggtgttggaatgaaatgaaggagtgtgcttgtaaattgcag

Basic information

species Vitis vinifera
transcript Vv07s0005g01440.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: LOC_Os03g52770.1 (Oryza sativa), 5'ss of exon 18
GTCAAATACCCAAAGGGCCCGGAGCCAGCTTCTGGAAAGCCATCTAGCAAAGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgta------tgattactgg--tggtgccattttaaataa----ttggtattggtgttggaatgaaatgaaggagtgtgcttgtaaattgcag--------
 ||||| || ||  | ||| | || ||  || | ||||  ||||||||||| || ||  |||| |||||||| || || || |||||||||||||||||||||      || |  ||    || |  |   ||||||||    ||  | ||    |    |  | |||||            |   |||||         
ATCAAACACACACCGTGCCAGAAGTCAATTTTTAGAAAATCATCTAGCAAAATTATTCGAGCAGAAAATGGAAATATTCACCAAAGTTGAATACACACAGgtagatatctgttcccttttctgttatctccttaaataacgtatttctttttacttctagaaaatatgaattccgtcaaggatgctttgcaccccttgtt

upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G023858_T01 (Zea mays), 5'ss of exon 18
GTCAAATACCCAAAGGGCCCGGAGCCAGCTTCTGGAAAGCCATCTAGCAAAGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgta------------tgattactggtggtgccattttaaa---taattggtattggtgttggaatgaaatgaaggagtgtgcttgtaaat-tgcag----
 ||||| || ||  | ||  | || ||| || | ||||  || || |||||||| ||| ||||||||||||| || || || |||||||||||||||||||||            | | ||       || | ||||| |    ||  | |||  |  || || |  | | |     ||      || || |  ||    
ATCAAACACACATCGTGCTAGAAGTCAGTTTTTAGAAAATCACCTGGCAAAGTTATTTGAGCAAAAAATGGAAATATTCACCAAAGTTGAATACACACAGgtaatctcccagaactaactatcccccttgtccttttagaagtaaaaagttatcagcttttgatttcattaatcttctggttcgttagatatttagacaa

upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA10G01660.1 (Glycine max), 5'ss of exon 19
GTCAAATACCCAAAGGGCCCGGAGCCAGCTTCTGGAAAGCCATCTAGCAAAGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattactggtggtgccattttaaataattggtattggtgttggaatgaaatga-aggagtgtgcttgtaaattgcag
||||||||| ||||||||  ||||||||||| ||||||  ||||| ||||| ||||||||||| ||| | || ||||| |||||||| ||||| |||||||||||  |  |  |  |     |      ||||   ||   | || ||  |   ||| |  | | | |||   ||| ||||
GTCAAATACTCAAAGGGCAAGGAGCCAGCTTTTGGAAACGCATCTTGCAAAATTGTTTAAGCAGAAAGTTGAAATTTTCACAAAAGTAGAATATACACAGgtatgtatgattattatattggtgatttaaatttaaataattctttgagagccgtgatatcattttccttacgaatcgcag

upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA02G01610.1 (Glycine max), 5'ss of exon 19
GTCAAATACCCAAAGGGCCCGGAGCCAGCTTCTGGAAAGCCATCTAGCAAAGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgat-tactggtggtgccattttaaataattggtattggtgttggaatgaaatgaaggagtgtgcttgtaaattgcag
||||||||| ||||||||  ||||||||||| | ||||  ||||||||||| ||||||||||| ||| | || ||||| |||||||| ||||| ||||||||||  | |  |  |  |     |      ||||   ||   |  | |   |  ||||    || | |||  |||| ||||
GTCAAATACTCAAAGGGCAAGGAGCCAGCTTTTCGAAACGCATCTAGCAAAATTGTTTAAGCAGAAAGTTGAAATTTTCACAAAAGTAGAATATACACAGgtattgtgtgattattatattggtgatttgaatttaaataattcgttgggagccatgatatcgtttccttacaaatcgcag

upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA19G40380.1 (Glycine max), 5'ss of exon 21
GTCAAATACCCAAAGGGCCCGGAGCCA---GCTTCTGGAAAGCCATCTAGCAAAGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattactggtggtgccatt---ttaaataattggtatt--ggtgttggaatgaaatgaa---------ggagtgtgcttgtaaattgcag
    ||||  |||| ||   ||| |||    ||  ||||||  |  ||||||||  |||||||||||||| | || ||||| |||||||| ||| | ||||||||||  | | | |      |||    |||   |      |||    |  | |  || ||  ||             | |||||  ||| |||||
---TAATATTCAAAAGGGAAGGAACCAACAACTCTTGGAAACACGCCTAGCAAAACTGTTTAAGCAAAAAGTTGAAATTTTCACAAAAGTAGAAAATACACAGgtattttgattcgaacaatcatcggattagtgaggcaaaatttaaataattgggtgcaaacaatattttatcaatctttgcttccaaaatgcag

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|30324169|gb|CD007431.1|CD007431
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|71889645|gb|DT038700.1|DT038700
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|30323970|gb|CD007232.1|CD007232
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32267461|gb|CD716424.1|CD716424
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|30325708|gb|CD008970.1|CD008970
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|110428353|gb|EC994822.1|EC994822
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|30327626|gb|CD010888.1|CD010888
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32269349|gb|CD718508.1|CD718508
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32269302|gb|CD718461.1|CD718461
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|110424565|gb|EC990929.1|EC990929
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32248389|gb|CD714208.1|CD714208
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32267654|gb|CD716617.1|CD716617
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32268218|gb|CD717377.1|CD717377
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32248728|gb|CD714547.1|CD714547
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32270860|gb|CD720019.1|CD720019
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|32268333|gb|CD717492.1|CD717492
EST:     AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
EST: gi|22011563|gb|BQ796597.1|BQ796597
EST:     AGTTG-TTAAGCAAATAATGGAGA-TTTTACAAAAGTTGAATACACACAG                         GAGTCAGTTGTAACTACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA
genomic: AGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattac ... taaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAATACCCAAAGGGCCCGGAGCCAGCTTCTGGAAAGCCATCTAGCAAAGTTGTTTAAGCAAAAAATGGAGATTTTTACAAAAGTTGAATACACACAGgtatgattactggtggtgccattttaaataattggtattggtgttggaatgaaatgaaggagtgtgcttgtaaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT