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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagcaccaatgcagactttcttcgtacaaaattccccttccagttctgtttagcattgtcctacattggagcaataacatgttttactaactcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAGGCATTCAACTCTGGTGATTTAGTCCGCTATCAAGAATTATGCCGTGTCC

Basic information

species Vitis vinifera
transcript Vv02s0012g02660.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 3
---------ccagcaccaatgcagactttcttcgtacaaaattccccttccagttctgtttagcattgtcctacattggagcaataacatgttttactaactcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAGGCATTCAACTCTGGTGATTTAGTCCGCTATCAAGAATTATGCCGTGTCC
              |    || ||  | | | | |   ||||| |  | |    |   | |  | || | |||  |||  |  |||     || || || |    |||||| || || ||||||||||||||||| || |||||||||||||| || ||||||||||| ||||||||| | || || |||||||||||||| || || |
gtgagtaattataaatttttggagcatctatccctttgaaatttctttacttcattcatctgtctttttactatgttgctgacatagt---ttataatatcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAGGCATTCAATTCTGGTGATCTGGTACGATATCAAGAATTATGTCGGGTGC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 3
-------------ccagcaccaatgcagactttcttcgtacaaaattccccttccagttctgtttagcattgtcctacattggagcaataacatgttttactaactcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAGGCATTCAACTCTGGTGATTTAGTCCGCTATCAAGAATTATGCCGTGTCC
              ||  |    || ||    | | | |   ||||| |  | |    |   |  | | |  | |||  ||||    | |   | |  || || |    |||||| || || ||| ||||||||||||| || ||||||||||| || || |||||||||||  ||||||||||| | |  |||||||||||||| || || |
gtgagtaattatatcaaaaattttggagcacctatcctt-tgaaatttctttacttcattcatccatcttcttactatgttggt-tgacatagtttaataatatcatgaacagATTAAGAGCCTTATGGGGACAAAGGTGGAATGGCTTTACTACATTCTGCAGGCATTCAATGCTGGTGATTTATTACAATATCAAGAATTATGTCGGGTGC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------------------------ccagcaccaatg-cagactttcttcgt-acaaaattccccttccagttct---gtt-tagcattgtcctacattggag------caataacatgttttactaactc--ctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAGGCATTCAACTCTGGTGATTTAGTCCGCTATCAAGAATTATGCCGTGTCC
                                                                                 |  | |   | |  |||   | || || |    |  |  |||| |  |||   ||| |||  |||      |||| ||      |  | ||||||   | |         |||| | |||||||| || || ||||| || || ||||| ||| | || || ||||||||||||  |||||||||||| |  ||||||||| |||||||||| |
gtaagttttccttcatcctcgacataaactactgttatattttcttgtgtagataaaaggcttcttgttgatctttaattgcttggatttacgatagatactgtttgtgagttgagacggcttctaactctcatgttatagttttgcttagaattgtagatggttctcttacatgtagcatttctctgatgacagTTGAAAAGTCTCCTTGGAACAAATGTGGAATGGCTCTACCACATTCTACAGGCATTCAACCATGGTGATTTAGTTCAGTATCAAGAACTATGCCGTGTGC

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|349823515|gb|FQ414925.1|FQ414925
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|351014718|gb|FQ437918.1|FQ437918
EST:     TGCTGGGAGATAATATCTATTACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|110694606|gb|EE071858.1|EE071858
EST:     CTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: CTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|110712232|gb|EE089617.1|EE089617
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|351030871|gb|FQ438907.1|FQ438907
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|110702107|gb|EE080439.1|EE080439
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|110711790|gb|EE088671.1|EE088671
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCA-TC                         ATAAAAAGTCTTCTGGGGAAAAAG-TTGA
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGA
EST: gi|351027874|gb|FQ448444.1|FQ448444
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|110729815|gb|EE106179.1|EE106179
EST:     TGCTGGGAGATA-TATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|110711621|gb|EE088310.1|EE088310
EST:     TGCTGGGAGATA-TATCTATAACTTTGGAGAACTGCTTGCTCATC-AATC                         ATAAAA-GTCT
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCT
EST: gi|351043427|gb|FQ451479.1|FQ451479
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|110712204|gb|EE089557.1|EE089557
EST:     TGCTGGGAGA-AATATCTATAACTTTGGAGAACTGCTTGCTCATCCA-TC                         ATAAAA-GTCTTCTGG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGG
EST: gi|349825445|gb|FQ419362.1|FQ419362
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|349825607|gb|FQ421706.1|FQ421706
EST:     TGCTGGGAGA-AATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCCTCTGGGGAACAA-GGTTGAGTGGCTTTACTA
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGA-CAAAGGTTGAGTGGCTTTACTA
EST: gi|351019814|gb|FQ439631.1|FQ439631
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
EST: gi|161718279|gb|FC066030.1|FC066030
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCT
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCT
EST: gi|110694939|gb|EE072388.1|EE072388
EST:     TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATC                         ATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG
genomic: TGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaagaattc ... actcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttagcattgtcctacattggagcaataacatgttttactaactcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAGGCATTCAACTCTGGTGATTTAGTCCGCTATCAAGAATTATGCCGTGTCC
                                        tactaac  putative branch site (score: 0)
                                              ctcctac  CT-rich tract
                            aataacatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagcaccaatgcagactttcttcgtacaaaattccccttccagttctgtttagcattgtcctacattggagcaataacatgttttactaactcctacagATAAAAAGTCTTCTGGGGACAAAGGTTGAGTGGCTTTACTATATACTCCAGGCATTCAACTCTGGTGATTTAGTCCGCTATCAAGAATTATGCCGTGTCC

-cagcacc
- - - - aatgcag
- - - - - - - - - - - - - acaaaat
- - - - - - - - - - - - - - - - - -cccttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataac