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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattcagtgcaatcgtgtattctcttttcattcttattgtctgtgggaagctgttctgctgtggatttgaaatcactaacatattgtttgttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTAG

Basic information

species Vitis vinifera
transcript Vv01s0127g00260.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G03530.1 (Glycine max), 3'ss of exon 5
--------------------------------------------atattcagtgcaatcgtgtattctcttttcattcttattgtctgtgggaagctgttctgctgtggatttgaaatcactaacatattgtttgttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTAG
                                             | || |    | | |||| |   | | | | | | |||     ||  ||    ||   |  ||   |||||  |       || | ||| |     |||||||||||  |||||||||||||| |||||||||||||  || | |||  ||
gtaaattcagttaattgttattttatgaacagattaagtttggagttttaaccatacttgtgtttatgcatattactttgattcgtgatgtaaatgaattggaccatgtgattgaatcc-----tgtactttttcta----cagATCAAGGGAGAAATTGAGGAGTTTCTCAAAGTGGTTTTCACTCTGTTTCAAG

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 5
-----------------------------------------------------atattcagtgcaatcgtgtattctcttttcattcttattgtctgtgggaagctgttctgctgtggatttgaaatcactaacatattgtttgttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTAG
                                                      | || |    | |||||| |   | | | | | | |||     ||  ||    ||   |  ||   |||||  |       || | ||| |     |||||||||||  |||||||||| ||| |||||||||||||  || | |||  ||
gtcaattcagtttaattgctaatttgttattttatgaacagattaagtttgaagtttttaccatactcgtgtttatgcatattactttgattcgtgatgtaaatgaattggaccatgtgattgaatcc-----tgtactttttcta----cagATCAAGGGAGAAATTGAGGAATTTCTCAAAGTGGTTTTCACTCTGTTTCAAG
















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|110730830|gb|EE108354.1|EE108354
EST:     CTTTTACCTCAGAAATTTGTGCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|111125104|gb|EE253722.1|EE253722
EST:     CACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|351054175|gb|FQ450257.1|FQ450257
EST:     CTTTTACCTCAGAAATTTGTGCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|110731355|gb|EE105692.1|EE105692
EST:     CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|110730143|gb|EE106883.1|EE106883
EST:     CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|349820930|gb|FQ408638.1|FQ408638
EST:     CTTTTACCTCAGAAATTTGTGCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|351035742|gb|FQ463587.1|FQ463587
EST:     CTTTTACCTCAGAAATTTGTGCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|349822202|gb|FQ412466.1|FQ412466
EST:     CTTTTACCTCAGAAATTTGTGCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|111125102|gb|EE253720.1|EE253720
EST:     CTTTTACCTCAGAAATTTGTGCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|294965669|gb|GW837268.1|GW837268
EST:     CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTT-ATCAAAGTG
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTG
EST: gi|71863321|gb|DT012376.1|DT012376
EST:     CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTTATCAA-GTGGTTTTTGCTTTATTTTT
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTT-ATCAAAGTGGTTTTTGCTTTATTTTT
EST: gi|161718453|gb|FC065040.1|FC065040
EST:     CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|351044803|gb|FQ449057.1|FQ449057
EST:     CTTTTACCTCAGAAATTTGTGCTCCGCTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA
EST: gi|161714091|gb|FC064386.1|FC064386
EST:     CTTTTACCTCAGAAATATGTGCTCCACTAGTTGCCACCCTTCCCTTGGAG                         ATCAAGGGAAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTCTATTTGTA
genomic: CTTTTACCTCAGAAATTTGTTCTCCACTAGTTGCCACCCTTCCCTTGGAGgtaatttata ... gttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggaagctgttctgctgtggatttgaaatcactaacatattgtttgttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTAG
                    atttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattcagtgcaatcgtgtattctcttttcattcttattgtctgtgggaagctgttctgctgtggatttgaaatcactaacatattgtttgttgattcagATCAAGGGGAAAATTGAGGAGTTTATCAAAGTGGTTTTTGCTTTATTTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - tgcaatc
- - - - - - - - - - - - - - - - - - - tgtctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactaac