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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtttcaattttgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC

Basic information

species Vitis vinifera
transcript Vv14s0060g02260.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------------------gcaagtttca--attttgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaacttgcctctaattaca------acagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC
                                                                                     |||| ||  |    ||  |||||     |||  |    |   | | | |     |||| ||| |||  |  |    || | ||  |||  |      | |||| |||||  | || ||||||||||||||||| |||||||| || || ||||| || || || || |||||||| || |||||||| |||||||||||||
gtacattgcttaataaatgttgaaagttcagtgttcctttttggaactggaaatattgacaaccatctctttagggaataatagagcaatttgtatcgcttcatgcatcaagcatgttacatttccatccatcttttccttttcataattt--atcattctttccatcctattttattgaatatagATTCAAGAGCTTGTGGAGGCAATTGTTTTGCCAATGACACACAAAGATCGGTTCCAAAAGTTGGGCATTCGCCCCCCCAAAGGAGTTCTTTTGTATGGAC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------gcaagtttcaat-----tttgtgcatattttatggaagt-----ggttgttgcttgtccgatttt---tgatactttcaactaaaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC
                                                                   | ||||  || |       | | ||||| | ||    ||      |||| || |||| |  | ||   || |   ||    |  |  ||     |   ||   ||||| |||||  | ||||| ||||| || ||||||||||| || ||||| ||||||||||| || || |||||||| || ||||| || |||||||| ||||
gtatttatttactttaaagatctaatgatgaaaacattagttaggatggtcaccattctgttgttatgtaagtagcagtaacttcatttccatatctcataagtgttcatcagttgctgtttgttcattgttatctgctctcttatgttctacttttatattgtctaatgcagATTCAAGAGCTTGTTGAAGCAATAGTATTGCCCATGACTCACAAGGACCGGTTTCAGAAGTTGGGAATTCGCCCCCCGAAAGGTGTTCTTTTGTACGGAC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 4
-gcaagtttcaattttgtgcatattttatg---gaagtggttgttgct-tgtccgatttttgatactttcaacta--aaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC
 | | ||  |  | ||       | ||||    ||| ||  |  |||  |||      | || ||| |  | ||    || ||      | | |    |||| |||||  | || |||||||||||  |||||||||||||||| || ||||| ||||| || |||||||| || || ||||| || |||||||| ||||
gggaggtccctttgttccatcagtcttatataagaaatgaataatgccgtgttgctcatctgttacatgtatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 4
-----------------gcaagtt-tcaattt--tgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC
                  ||| || || ||    | |   | ||||    |  |     | | |     |  ||  |||  | | | | | ||||||    |     ||||||||||||||||||||||| |||||||||||||| |||||    ||||||||||| || ||||||||  |||| ||||| || |||||||| || |||||||
gtgcactataattaccgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccgatgatgtgatcaataacttggtctttgc--caacagATCCAAGAATTAGTTGAAGCAATTGTTTTGCCAATGACCTGCAAGGAGCGGTTCCAAAAATTAGGAGTTCGTCCACCGAAGGGAGTGCTCTTATATGGAC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 4
gcaagtttcaattttgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC
|  || ||   || |   |||| ||||| ||||   ||      | |  |   || | || ||        |  |    || |||  |||||||| |||||||||||||| || ||||||||||||||||| || ||||||||||| || || |||||  |||| || || || |||||||| ||||||||||
gtgagctttggttcttgccataatttattgaagcactt----tcttttgggggttaggtaattgatctctcaggtcatttc-aat--caacagATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGGTTCCAAAAGTTAGGAGTTCGTCCTCCCAAGGGAGTGCTGTTGTATGGAC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 4
gcaagtttcaattttgtgcatattttatggaagtggttgtt-------gcttgtccgattttt--gatactttcaactaaaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC
|  || ||   || |   | || ||||| ||||   |||||       | |  | | || | |  | |  ||||||    ||||||    |  |  |||||||| |||||||||||||| || ||||||||||||||||| || |||||||| || || || |||||  |||| || || || |||||||| || |||||||
gtgagctttggttcttgccttaatttattgaagcccttgtttgggttagttaatgcaatctctcaggtcatttcaat---aacttggtcttcct--caacagATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGATTCCAAAAGTTAGGAGTTCGTCCTCCCAAGGGAGTGCTGTTATATGGAC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 2
-----------------gcaagtt-tcaat--------tttgtgcatattttatggaagtggttgttgcttgtccga-tttttgatactttcaactaaaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC
                 |||| || |||||        | | |   | |||  |   | |     ||   |  | |  | | ||||| | | | | | ||||||          ||||||||||||||||  |||||  | ||||||||||| || || || ||||||||||| |||||||| ||  || | ||||| || |||||||| || |||||||
gtactctataattacgggcaatttatcaatgcactctttctttctttttttcttcttatttacaattaggtaacagggtctctgatagtgtgatcaataacttggtctctgc--caacagATCCAAGAATGGGTTGAAACTATTGTTTTGCCAATTACCCACAAGGAGCGGTTCCAGAAATTTGGAGTTGGTCCACCGAAGGGAGTGCTCTTATATGGAC

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|110724320|gb|EE100046.1|EE100046
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|110384620|gb|EC949072.1|EC949072
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|71859210|gb|DT008265.1|DT008265
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|110711112|gb|EE087285.1|EE087285
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|71857850|gb|DT006905.1|DT006905
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGGCA-TTGTTTTGCCCATGACAC
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGG-CAATTGTTTTGCCCATGACAC
EST: gi|110718444|gb|EE095285.1|EE095285
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|110685213|gb|EE063376.1|EE063376
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|71863186|gb|DT012241.1|DT012241
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|110724441|gb|EE100272.1|EE100272
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|110722856|gb|EE099502.1|EE099502
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|71861858|gb|DT010913.1|DT010913
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTT
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTT
EST: gi|30255105|gb|CB971552.1|CB971552
EST:     ATGAAAAACCAGCAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|30252235|gb|CB969786.1|CB969786
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|110732813|gb|EE108430.1|EE108430
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAACAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|34549827|gb|CF518059.1|CF518059
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|34544589|gb|CF512821.1|CF512821
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|30252226|gb|CB969777.1|CB969777
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
EST: gi|71879123|gb|DT028178.1|DT028178
EST:     ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAG                         ATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG
genomic: ATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttca ... attacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcttgtccgatttttgatactttcaactaaaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC
            atttttgatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtttcaattttgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG