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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttttctaacagctgaattttcctcccctttgttggttctgcgatgttttgttgaattttgggtgattttattctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGAGCATACTGGGGATTGACCACTCTAGATCTTCTTGGAAAGCTGGAAATAG

Basic information

species Vitis vinifera
transcript Vv12s0134g00150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G11710.1 (Glycine max), 3'ss of exon 2
----gtgtgttttcta---acagctgaattttcctcc---cctttgttggttctgcgatgttttgttgaattttgg-------gtgattttattctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGAGCATACTGGGGATTGACCACTCTAGATCTTCTTGGAAAGCTGGAAATAG
    ||||| || | |   | |  |  || | | | |   | |   ||  ||||   |  | || || |||  |         ||  ||||||  |   |||||||| ||| | |||||||| || ||||  |||||||| ||||||||||| ||||||||||||||||||||||| |||||||| ||||||||  |    |
gtgggtgtgcttcccatttatatatatatatacatacatacatacattctttctcaaaactcttctttaatgcttaaaaggttgtccttttatggtttccagAGGAAAGATAACTTTGAATCTGTAGTAATGGAGCATCTGAGAATGAATGGGGCATACTGGGGATTGACCACTCTGGATCTTCTAGGAAAGCTTCATTCTG

upper sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G28630.1 (Glycine max), 3'ss of exon 1
gtgtgttttctaacagctgaattttcctcccctttgttggttctgcgatgttttgttgaattttgggtgattttattctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGAGCATACTGGGGATTGACCACTCTAGATCTTCTTGGAAAGCTGGAAATAG
||||| | |    |   |  ||         | |||     ||| |  |  |   |  ||  |||  |  ||||||  |   |||||||| ||| | |||||||| || ||||  |||||||||||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||  | |  |
gtgtgctgtgcttcccatttatacatggatgccttgcaaactcttctttaatgcttaaaaggttg--tccttttatggtttccagAGGAAAGATAACTTTGAATCTGTCGTAATGGAGCATCTAAGAATGAATGGGGCATATTGGGGATTGACCACTCTGGATCTTCTAGGAAAGCTTCATACCG

upper sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G12210.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------gtgtgttttctaacagctgaattttcctcccctttgttggttctgcgatgtttt---gttgaattttgggtgat-tttattctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGAGCATACTGGGGATTGACCACTCTAGATCTTCTTGGAAAGCTGGAAATAG---
                          |   |||||||  | | | |  |  |      | | | | || ||   |  |||    |||  |||||  |  | |||| | | || ||| ||| ||   |||||| || ||||| |  || ||||||||||||||||| |||||||||||| | |||||||| ||  | ||||  ||||| |     |   
gtacctagaaactgtatagaacctttgctcgttttct--ctgtttatgtcactgtgattgtatagcttatgttcttcttttcaattgctttttgaattttatttaatttgct-agaagAAAGAGAGTTTTGAGTCTGTGGTGATGGATCATCTAAGAATGAATGGTGCATACTGGGGACTCACCACTCTCGACTTACTTGACAAGCTCGGCTGTGTTT

upper sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G12210.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------gtgtgttttctaacagctgaattttcctcccctttgttggttctgcgatgtttt---gttgaattttgggtgat-tttattctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGAGCATACTGGGGATTGACCACTCTAGATCTTCTTGGAAAGCTGGAAATAG
                          |   |||||||  | | | |  |  |      | | | | || ||   |  |||    |||  |||||  |  | |||| | | || ||| ||| ||   |||||| || ||||| |  || ||||||||||||||||| |||||||||||| | |||||||| ||  | ||||  ||||| |     |
gtacctagaaactgtatagaacctttgctcgttttct--ctgtttatgtcactgtgattgtatagcttatgttcttcttttcaattgctttttgaattttatttaatttgct-agAAGAAAGAGAGTTTTGAGTCTGTGGTGATGGATCATCTAAGAATGAATGGTGCATACTGGGGACTCACCACTCTCGACTTACTTGACAAGCTCGGCTGTG

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|349826932|gb|FQ419023.1|FQ419023
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|161712241|gb|FC061615.1|FC061615
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|351047683|gb|FQ455080.1|FQ455080
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|351032822|gb|FQ461711.1|FQ461711
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|349810206|gb|FQ401652.1|FQ401652
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|161721200|gb|FC071051.1|FC071051
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|349817650|gb|FQ407639.1|FQ407639
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|349809279|gb|FQ399053.1|FQ399053
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|351015754|gb|FQ431709.1|FQ431709
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|351045119|gb|FQ449373.1|FQ449373
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAGGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|349815323|gb|FQ400478.1|FQ400478
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|349807995|gb|FQ402386.1|FQ402386
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA
EST: gi|351045348|gb|FQ451796.1|FQ451796
EST:     GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAG                         AGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAGGAATGAATGGA
genomic: GAGAGCTGGAAGCTGAGAAACATGTTCAATACATTTTATTAGTTGAAAAGgtgtgttttc ... ttctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttgttggttctgcgatgttttgttgaattttgggtgattttattctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGAGCATACTGGGGATTGACCACTCTAGATCTTCTTGGAAAGCTGGAAATAG
                                        ttttattct  CT-rich tract
                    ttttgttgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttttctaacagctgaattttcctcccctttgttggttctgcgatgttttgttgaattttgggtgattttattctactcagAGGAAGGATGATTTTGAATCAGTGGTAACAGAGCATCTAAGAATGAATGGAGCATACTGGGGATTGACCACTCTAGATCTTCTTGGAAAGCTGGAAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA