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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatggtaaaccatgttcttttttgttttttttttaaagatttttttttttttaatttgttggtaaataatgaaacttaaaattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC

Basic information

species Vitis vinifera
transcript Vv16s0013g01510.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 1
ggatggtaaac-catgttcttttttgttttttttttaaagatttttttttttttaatttgttggtaaataatgaaacttaa--aattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC
   ||  |  | | | |||  |     |  ||  ||||     ||  ||    | || ||    ||  |  ||      ||  | | || ||  || || |||||||||||||| || || ||||| || ||||| ||||| ||||| ||||| |||||||| ||||| || |||||||||||||| || |  ||||||||||
---tgtcatgcgctttttccatccgactcattgattaagctgcttaattccaattatctgcctctagttcctggtttgcaatcattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC

upper sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 1
ggatggtaaac-catgttcttttttgttttttttttaaagatttttttttttttaatttgttggtaaataatga--aacttaaaattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC
   ||  |  | ||| |||  | |   |  ||  ||||     || |||    | || ||    ||  | |||     |   || | || ||  || || |||||||||||||| || || ||||| || ||||| ||||| ||||| ||||| |||||||| ||||| || ||||| |||||||| || |  || |||||||
---tgtcatgcacatattccatctgactcattgattaagctgcttatttccaattatctgcctctagttcatggtttgcaccaattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC

upper sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G07590.1 (Arabidopsis thaliana), 3'ss of exon 1
ggatggtaaaccatgttcttttttgtttttt---ttttaaagatttttttttttttaatttgttggtaaataatgaaacttaaaattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC
   || ||||   ||    ||||    ||     |  ||||  |  ||    ||||  ||| ||  ||  || | |   | ||  || |   |    || ||||||||||| || || || ||||| ||||| ||||||||||| || ||||||||||||||||| ||||| ||||||||||| ||||| | ||| ||||| |
---tgctaaattttggaacttttaaccttagagatgataaatgtcgttgaagtttttttttctttctatgtactaatcttcaatgttatggatgtgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC

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|110700942|gb|EE078040.1|EE078040
EST:     TATCGCTTATT                         GTTGTCGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGC
genomic: TATCGCTTAAGgtatttatca ... tctgatacagGTTGT-GCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGC
EST: gi|110700943|gb|EE078041.1|EE078041
EST:     TATCGCTTAAG                         GTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCT
genomic: TATCGCTTAAGgtatttatca ... tctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCT
EST: gi|161716527|gb|FC065224.1|FC065224
EST:     CTGTTGCAGTTGATTATCGTCTTGTGATTAGGGATGTGTTATCGCTTAAG                         GTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCT
genomic: CTGTTGCAGTTGATTATCGTCTTGTGATTAGGGATGTGTTATCGCTTAAGgtatttatca ... tctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCT
EST: gi|161718383|gb|FC066306.1|FC066306
EST:     CTGTTGCAGTTGATTATCGTCTTGTGATTAGGGATGTGTTATCGCTTAAG                         GTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCT
genomic: CTGTTGCAGTTGATTATCGTCTTGTGATTAGGGATGTGTTATCGCTTAAGgtatttatca ... tctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttaatttgttggtaaataatgaaacttaaaattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC
                                            ttctgat  putative branch site (score: 3)
                                     ttttattttct  CT-rich tract
     tttaatttgttggtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatggtaaaccatgttcttttttgttttttttttaaagatttttttttttttaatttgttggtaaataatgaaacttaaaattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - -aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttaaaa