Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatctcaccatttgatgtgaaagagatttttttttttttggtacagatttatatcattctgcgtgtatagttatgagattcgatccatgacttggtctatgtgtttgttgtttaatgttggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGTGTCCTGTAACTGGAAAGAGGATTCAAGGG

Basic information

species Vitis vinifera
transcript Vv01s0026g02410.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g02410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G41280.1 (Glycine max), 3'ss of exon 1
----gtcatctcaccatttgatgtgaaagagatttttttttttttggtacagatttatatcattctgcgtgtatagttatgagattcgatccatgacttggtctatgtgtttgttgtttaatgttggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGTGTCCTGTAACTGGAAAGAGGATTCAAGGG
     | | ||| |            |     |  ||| || |     || |     | || || ||||      |    |||    | ||||  | |   | |   |||  | |   | ||  | ||||  |||||| ||||| || ||||||| ||| ||||||||||| | ||| || ||||| ||||| |||||||||||||||||||||
gtaaataaactctcttcgctcgcctcacatcgtcgtttattctcactcacggcgcgttgtcgttttgcgcc----gccgcgagg---gctccaaaaatatattttaatgtgcggttgctgattgttgaatgcagGTGGCAAGCTTGTTTATCAGACCACGAAGAAGAGGGCCAGCGGACCCAAGTGCCCTGTCACTGGAAAGAGGATTCAAGGG

upper sequence: Vv01s0026g02410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G14980.1 (Glycine max), 3'ss of exon 1
gtcatctcaccatttgatgtgaaagagatttttttttttttggtacag--atttata-tcattctgcgtgtatagttatgagattcga----tccatgacttggtctatgtgtttgttgtttaatgttggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGTGTCCTGTAACTGGAAAGAGGATTCAAGGG
                    | ||    | ||   |   || | |  |   |||||  ||| ||   | || | ||| || |   |||    || |  | | |       |||  | ||  |  |  | ||||  |||||| ||||| || ||||||| ||| ||||||||||| | ||| || ||||| ||||| |||||||||||||||||||||
--------------------gtaaactgtcttcgctcgcttcgcatcgtcgtttattctcactcatggcgtgtcgtt-tgcgccgcgagtgttctaaaaatagactgtaatgtgcggtggctggttgttgaatgcagGTGGCAAGCTTGTTTATCAGACCACGAAGAAGAGGGCCAGCGGACCCAAGTGCCCTGTCACTGGAAAGAGGATTCAAGGG

upper sequence: Vv01s0026g02410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G11920.1 (Glycine max), 3'ss of exon 1
---gtcatctcaccatttgatgtgaaagagatttttttttttt-tggtacagatttatatcattctgcgtgtatagttatgagattcgatccatgacttggtctatgtgtt-tgttgtttaatgttggaa---tttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGTGTCCTGTAACTGGAAAGAGGATTCAAGGG
    |||  || |  || |         |     | ||   || || | |  ||    |  ||| |   | | || || || |  |  ||   |    ||     | |||| ||||   | |||| ||||   |  |||||| ||||| || ||||||| ||||||||||||||| | ||| || ||||| || || ||||| ||||||||||| |||
gtaatcaaatccctcttcggaacccctcactcactcttcgattatgcttcgaatcggaacaatttttgctttttaattttgggtattaattggt--tctgacgggtatgttgtgtttggtgatgtgggaataatgcagGTGGGAAGCTCGTTTATCAGACCACCAAGAAGAGGGCCAGCGGGCCCAAGTGCCCCGTCACTGGCAAGAGGATTCAGGGG

upper sequence: Vv01s0026g02410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G05740.1 (Glycine max), 3'ss of exon 1
--------gtcatctcaccatttgatgtgaaagagattt--ttttttttttggtacagatttatatcattctgcgtgtatagttatgagattcgatccatgacttggtctatgtgtttgttgtttaatgttggaat---ttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGTGTCCTGTAACTGGAAAGAGGATTCAAGGG
         ||    |  || |   | ||     |||        |||||   |     ||| | |  || |      | |||| |  |  |  ||   |      |  || || ||  ||| ||  ||| |||||     |||||| ||||| || |||||||  |||||||||||||| | ||| || ||||| || || ||||| ||||||||||| |||
gtaatcaaatccctccctcactgattatgcttcggatcggaacaatttttgtttttgtttttgttttgttttaaaaaaaaagtttttggtattaattggttctgctgggtacgtcttgtttggttc-tgtgggaataatgcagGTGGGAAGCTCGTTTATCAGACTACCAAGAAGAGGGCCAGCGGACCCAAGTGCCCCGTCACTGGCAAGAGGATTCAGGGG

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|110715774|gb|EE094207.1|EE094207
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|349827592|gb|FQ422460.1|FQ422460
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|27582239|gb|CB004934.1|CB004934
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|71871363|gb|DT020418.1|DT020418
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110707256|gb|EE083500.1|EE083500
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110695694|gb|EE074007.1|EE074007
EST:     CCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: CCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110703427|gb|EE080263.1|EE080263
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|161716131|gb|FC066487.1|FC066487
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110691194|gb|EE069016.1|EE069016
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|37187841|gb|CF607194.1|CF607194
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|30134974|gb|CB920312.1|CB920312
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|352785847|gb|FQ475850.1|FQ475850
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110419706|gb|EC985955.1|EC985955
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|71875792|gb|DT024847.1|DT024847
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|71867822|gb|DT016877.1|DT016877
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110400132|gb|EC966677.1|EC966677
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|71866217|gb|DT015272.1|DT015272
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110732670|gb|EE108161.1|EE108161
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|349824962|gb|FQ406534.1|FQ406534
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110365512|gb|EC928620.1|EC928620
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|71866026|gb|DT015081.1|DT015081
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|352789622|gb|FQ476220.1|FQ476220
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCCAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
EST: gi|110717929|gb|EE094214.1|EE094214
EST:     GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAG                         GTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT
genomic: GCACAGCTATGCCACTAAGTCCAACCAGCACAGGGTCGTCAAAACCCCAGgtcatctcac ... tggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagattcgatccatgacttggtctatgtgtttgttgtttaatgttggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGTGTCCTGTAACTGGAAAGAGGATTCAAGGG
                                    gtttaat  putative branch site (score: 4)
                                  ttgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatctcaccatttgatgtgaaagagatttttttttttttggtacagatttatatcattctgcgtgtatagttatgagattcgatccatgacttggtctatgtgtttgttgtttaatgttggaatttagGTGGAAAGCTGGTGTATCAGAGCACCAAGAAGAGGGCAAACGGTCCTAAGTGTCCTGTAACTGGAAAGAGGATTCAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT