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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctttcctttttctctgtttggtttctcagagagtaaagcccttcctttttcatcaggctttgatattatacaaaaaaacgggttttgcttttgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGACCATGAGCGTGTTGTCGATTGCACTACTCCTAATTTTAATGG

Basic information

species Vitis vinifera
transcript Vv10s0071g01040.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0071g01040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G00250.2 (Glycine max), 3'ss of exon 2
gtctttcctttttctctgtttggtttctcag-agagtaaagcccttcctttttcatcaggctttgatattatacaaaaaaacgggttttgcttttgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGACCATGAGCGTGTTGTCGATTGCACTACTCCTAATTTTAATGG
                         ||| || |   ||   |||||  ||||||||||   |||  | || |||||         || || ||||||| | ||||||||||||||||||||||| || ||| | |||||||||||||| ||||| || ||||||||||| |||||||||||||| |||||||||||
------------------------gtcttagtaccctactaccctttatttttcatcattgttttttgtt-tacaat--------ttctgtttttgtttcacagttcagAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGATCACGAGCGTGTTGTTGATTGCACTACTCCCAATTTTAATGG

upper sequence: Vv10s0071g01040.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G40390.2 (Glycine max), 3'ss of exon 1
gtctttcctttttctctgtttggtttctcag-agagtaaagcccttcctttttcatcag------gctttgatattatacaaaaaaacgggttttgcttttgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGACCATGAGCGTGTTGTCGATTGCACTACTCCTAATTTTAATGG
                         ||| || |   ||   |||||  ||||| ||||       | |||| | ||||        ||   || || ||||||| | ||||||||||||||||||||||| || ||| | |||||||||||||| ||||| |||||||  ||||| |||||||||||||| |||||||||||
------------------------gtcttagtaccctactaccctttatttttaatcatttttttgttttgtttttatttttgtttacaatttctgtttttgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGATCATGAGCTAGTTGTTGATTGCACTACTCCCAATTTTAATGG
















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|110384025|gb|EC948438.1|EC948438
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|33408217|gb|CF213844.1|CF213844
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|352795434|gb|FQ476549.1|FQ476549
EST:     GAGCTTGCCTCCGTTGCCGGCTCCTCCAAACCCTAC-ATCCG                         TTCCGAGAGTCCGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: GAGCTTGCCTCCGTTGCAGGCTCGT-CAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|110688876|gb|EE067932.1|EE067932
EST:     CAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: CAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|30296227|gb|CB973021.1|CB973021
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|33408305|gb|CF213932.1|CF213932
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|110407013|gb|EC972604.1|EC972604
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|351049428|gb|FQ450029.1|FQ450029
EST:     ACGAGCTCAGAGCTTGCCTCCGTCGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|110412486|gb|EC978236.1|EC978236
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|294964123|gb|GW837926.1|GW837926
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|30296163|gb|CB972957.1|CB972957
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|30296421|gb|CB973215.1|CB973215
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|26258793|gb|CA809856.1|CA809856
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|26264415|gb|CA815478.1|CA815478
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTTCGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
EST: gi|77585520|gb|DV221849.1|DV221849
EST:     ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAG                         TTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC
genomic: ACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctt ... tgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcatcaggctttgatattatacaaaaaaacgggttttgcttttgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGACCATGAGCGTGTTGTCGATTGCACTACTCCTAATTTTAATGG
           ctttgat  putative branch site (score: 5)
                                    ttttgcttttgttcc  putative PPT
            tttgatattatacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctttcctttttctctgtttggtttctcagagagtaaagcccttcctttttcatcaggctttgatattatacaaaaaaacgggttttgcttttgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGACCATGAGCGTGTTGTCGATTGCACTACTCCTAATTTTAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA