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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaaaactgatattctcatcttaacgttggcacag

Basic information

species Vitis vinifera
transcript Vv09s0002g05950.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 7
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcc---tgtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaa-aactgatattctcatcttaacgttggcacag
 || ||||| || ||||||||||| || |||||||||||||| ||||| || ||||| |||||||| |||||||||||||| |||||||| ||||| || ||||  | |   || | | |     | ||  | ||   | || |     |     || ||    ||     ||| |  || |  |  |  |||||
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTCCTGCCACTGAAGCCCAGgtaagtttctaatgcgttgttgggctcttacagttgtgacatgttgggttagcattaagggcctaagcatgattgttgtcatc-ctctaccacag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatgg--aaaaactgatattct----catcttaacgttggcacag---
 || ||||| || ||||||||||| || ||||| |||||||| ||||| || ||||| || || |||||||||||||| || || || |||||||| || ||| | ||||||  ||    |||  |  | | ||||   ||  || | ||| | |||   |  |||||  |  |     || || |  |    |  |   
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagc-tcctgtttttgagttgt-ctgcactctgcaccgtt--tagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G032367_T03 (Zea mays), 5'ss of exon 6
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaaaactgatattctcatcttaacgttggcacag
||| || || || ||||||||||| || ||||| |||||||| |||||||  ||||| |||||||||||||| |||||||| ||||| || ||||| || ||||  |  |    ||     ||  |||||      | |||   | ||  ||  | | |  |  | |   |   |  ||       |||||
CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactattactgtt-----gttgtttatccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G158479_T02 (Zea mays), 5'ss of exon 6
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaa-catcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaaaactgatattctcatcttaacgttggcacag
||| ||||| || ||||||||||| || ||||| ||||| || ||||| |  ||||| |||||||||||||| |||||||| ||||| || ||||| || |||| |   ||||  | |  ||   | |  ||||| |    |  |   | |||  |  |||   ||||   ||||| ||  |   |      
CTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACACCTGCAACTGAAGCCCAGgtaaactaactgtcatgttgattcctgtacttttgaa----ttgtggggcaggact--aaagtttgat-cactcatattccctcag------

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 6
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct----------gtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaaaactg--------atattctcatcttaacgttggcacag
||||||||||||||| ||||||||||| || |||||||| |||||||| |  ||||| |||||||| |||||||||||||||||||| |||||| | || ||| | |  |          ||| ||||| |  || | ||       |||   ||    |  |  ||||||| |         ||||| |    |     |||  ||||
CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttatttgttgaggagtggtttcagtaaatctcatgacattgattatctat--gaacttcggaaaaattatgcaaaatatatttttggttactttttgctacag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 6
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgct----------ttcaatgtattttattttgcaaatttcatact-------gaaggtatggaaaaactgatattctcatcttaacgttggcacag
||||||||||||||| ||||| ||||| || |||||||| |||||||| |  |||||||||||||| |||||||||||||||||||| |||||| | || |||   |  | || |          |||| |  || | ||       |||   ||         ||||   |  |  || | || || |  |  ||   |||  ||||
CTATAATCCTTATTTTCCTGGCGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacttttgtttgttgaggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttatatt-ttgctacag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA19G24620.2 (Glycine max), 5'ss of exon 6
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaat-ttcatactgaaggta--tggaaaaactgatattc---tcatcttaacgtt-ggcacag
 ||||||||||| || |||||||| ||||| || ||||| |||||||| |  ||||||||||| || |||||||||||||||||||| |||||||| || |||  ||  | || ||     | | |   ||| | |||| ||| |||  |  | |  |||||||| ||    ||   | || |||| ||| |   |||
TTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCCCTGCTACAGAAGCTCAGgtattatatt-tgtttctggaggaatg-gtttagtaaatcttcttacaaatagaaattggaaaaaatgtagctcattttattttaatgtttgttgcag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G06700.2 (Glycine max), 5'ss of exon 6
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaa---ggtatggaaaaactgatat--tctcatcttaacgtt-ggcacag
 ||||||||||| || |||||||| ||||| || ||||| |||||||| |  ||||||||||| || |||||||||||||| ||||| |||||||| || |||  |   |    | |  | | || |  ||| | |||| |  |    ||   | | ||  | ||   |  |  | |  |||||| ||| |   |||
TTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACTCCTGCTACAGAAGCTCAGgtattaaatttgcttctggaggaatatggtttagtaaatcttcttaaaaatgggatttgatagaatctagctcattttctcttaatgtttgttgcag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 5
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaaaactgatattctcatcttaacgttggcacag------------------------------------
||| |||||||||||||||||||| ||||| |||||||| |||||||||| |||||  ||||| || ||||||||||| || ||||| ||||||||||| || |  |    |    | ||   | |  | |||||| |   ||||   ||| | |   | |  |||  ||  |       |  |   | |                                     
CTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTCCTGCAACAGAAGCACAGgttagttttcctctgcttaagaaaat--aatttgcagac--cata---aagttttatcagatttgacctttcctctgagtcaattatataatctttaatttttctttttttaaaaaacatgatgcag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 6
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaa-------aaactgatattctcatcttaacgtt--ggcacag
||| ||||||||||||||||| || ||||| |||||||| ||||||||||  ||||  |||||||||||||||||||||  ||| |||||||| ||||| || |  |    | |  | ||  |||   |   |  |  |||    || | ||||  |         |   | ||  | | | ||| || ||  ||  |||
CTACAATCCTTATTTCCCTGGGGGAGCAATTGCTATGCCGAAAATGCTCAATGATGAAGCTGTTGAGTATGAAGATGGTGTCCCCGCCACAGAGGCACAGgttatttttcctccacttaaaatataagaacataaatctttatgccttatggtactgtcctttctcagtgtcatgatataaactttactttacggtgcag

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|110377968|gb|EC943074.1|EC943074
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|110423661|gb|EC990009.1|EC990009
EST:     TTGATGGTGCTGTTGAGTATGAAGATGGCACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|30321061|gb|CD004323.1|CD004323
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|110698992|gb|EE077122.1|EE077122
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|34550509|gb|CF518727.1|CF518727
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAG
EST: gi|349813644|gb|FQ413878.1|FQ413878
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|110694100|gb|EE070911.1|EE070911
EST:     TTGATGGTGCTGTTGAGTATGAAGATGGCACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|351028222|gb|FQ426123.1|FQ426123
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAAAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|110428516|gb|EC994990.1|EC994990
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|34547391|gb|CF515623.1|CF515623
EST:     TCGACGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|34550428|gb|CF518646.1|CF518646
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAG
EST: gi|351033244|gb|FQ462016.1|FQ462016
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|34547301|gb|CF515533.1|CF515533
EST:     TCGACGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|30320467|gb|CD003729.1|CD003729
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|349808524|gb|FQ405668.1|FQ405668
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|110417035|gb|EC983057.1|EC983057
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|351017876|gb|FQ436229.1|FQ436229
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTG
EST: gi|110378867|gb|EC944022.1|EC944022
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
EST: gi|349809896|gb|FQ398521.1|FQ398521
EST:     TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCCGCCACAGAAGCACAA                         ATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG
genomic: TCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct ... gttggcacagATGGGGAAAGATGTTGTCACATTTTTATCATGGGCTGCAGAGCCAGAAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaaaactgatattctcatcttaacgttggcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC