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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttctttgcctttggtttagccagaatctgaaaattctttcaaagcaaatagttccattatgggtgttatgtgaaactaaaacgtgttttctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGCTTCAACAAGGAGAGGATGAAACAGAATCTGGAGATATTTGATTGGGAAC

Basic information

species Vitis vinifera
transcript Vv01s0011g06470.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g37490.1 (Oryza sativa), 3'ss of exon 3
-----------atttctttgcctttggtttagccagaatctgaaaattctttcaaagcaaatagttccattatgggtgttatgtgaaactaaaacgtgttttctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGCTTCAACAAGGAGAGGATGAAACAGAATCTGGAGATATTTGATTGGGAAC
           || |   | ||| || | | |  |  |   | || | |||  | |  ||| |||    |  |  || | || | ||           ||||    |  |||| |  ||||||||| || ||||| |||| |||| ||   |    ||||||| ||||||||||||| ||||||||||||| |||||||| || ||||| |
aatacaagtacatatggatacctatgttgttgataacaaa-ggaactacttcgataataaaaagtcttttagttagtctgatataaat----------ttttaccctttagGTGTCATTGAGATGGATTCATGAGCAAGGAGTGACCCCAATCCCCAAGAGCTACAACAAGGAGAGGCTGAAACAGAATCTTGAGATATTCGACTGGGAGC
















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|349813733|gb|FQ413967.1|FQ413967
EST:     TGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCCAG                         GTTTGTTTGAAATGGGTTTATGAGGAAGGGGTGAGCCTTCT
genomic: TGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCC-AGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCT
EST: gi|351035169|gb|FQ458526.1|FQ458526
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGGTTATGAAGAAGGGGTGAGCCTTC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTC
EST: gi|351048963|gb|FQ449806.1|FQ449806
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAA                         GTTTGTTTGAGATGGTTTTATGAAGAAGGGGTGAGCCTT
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTT
EST: gi|351053660|gb|FQ440169.1|FQ440169
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
EST: gi|351053726|gb|FQ441492.1|FQ441492
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
EST: gi|349817504|gb|FQ407294.1|FQ407294
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
EST: gi|351032689|gb|FQ462403.1|FQ462403
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGG
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGG
EST: gi|349822747|gb|FQ398134.1|FQ398134
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGT
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGT
EST: gi|110384776|gb|EC949237.1|EC949237
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAATTCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
EST: gi|351013364|gb|FQ425069.1|FQ425069
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTAT
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTAT
EST: gi|351035143|gb|FQ458500.1|FQ458500
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAAC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
EST: gi|352794471|gb|FQ481704.1|FQ481704
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTA
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTA
EST: gi|351032310|gb|FQ461563.1|FQ461563
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
EST: gi|349814016|gb|FQ414250.1|FQ414250
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGGTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
EST: gi|349821554|gb|FQ408113.1|FQ408113
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGC
EST: gi|349814748|gb|FQ409971.1|FQ409971
EST:     GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTTCT-GTGAAGAG
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTT-CTTGTGAAGAG
EST: gi|351031264|gb|FQ445289.1|FQ445289
EST:     GTGAGGTGCTCAAAGAAATTGCCAAAGAAACAGGAAAATCAATTGCCCAG                         GTTTGTTTGAGATGGGT
genomic: GTGAGGTGCTCAAAGAAATTGCCAGAGAAACAGGAAAATCAATTGCCCAGgtaaatactc ... tctgttgaagGTTTGTTTGAGATGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaatagttccattatgggtgttatgtgaaactaaaacgtgttttctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGCTTCAACAAGGAGAGGATGAAACAGAATCTGGAGATATTTGATTGGGAAC
                              aactaaa  putative branch site (score: 2)
                                          ttttctgtt  putative PPT
                             aaactaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttctttgcctttggtttagccagaatctgaaaattctttcaaagcaaatagttccattatgggtgttatgtgaaactaaaacgtgttttctgttgaagGTTTGTTTGAGATGGGTTTATGAGGAAGGGGTGAGCCTTCTTGTGAAGAGCTTCAACAAGGAGAGGATGAAACAGAATCTGGAGATATTTGATTGGGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - -tgccttt
- - - - - - - - -ttagcca
- - - - - - - - - - - - - - - gaaaatt
- - - - - - - - - - - - - - - - - - - - - aaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa