Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAACAATAGCTTCTTCAGATGAGGCTGAACATGGCCTGGCATGTCCAAACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagattacatcttatgttatctattacgcaatctatagaaaagtgtcttgataggactttgagaaactaaacatcggttcaaaggccttcccttg...

Basic information

species Vitis vinifera
transcript Vv09s0002g05950.t01
intron # 2
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 2
lower sequence: GLYMA16G06700.1 (Glycine max), 5'ss of exon 4
TTGCAACAATAGCTTCTTCAGATGAGGCTGAACATGGCCTGGCATGTCCAAACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagc--agattacatcttatgttatctattacgcaatctatagaaaagtgtc-ttgataggactttgaga-aactaaacatcggttcaaaggccttcccttg
|| ||||||| ||  |  | ||||| ||||||||||||||||||||||||| |||||||||||||||||  || ||||| ||||||||||| || ||||||||||    | ||  || ||   |    | |       | |    || | | |  || |    | |   | | ||   ||  |     |    |  || |    
TTTCAACAATGGCAGCAGCTGATGAAGCTGAACATGGCCTGGCATGTCCAAGCTATCCATGGCCTCACAAGGGAATTCTTAGTTCATATGATCACGCTTCgtaagtttggcttgaattttccctatattttcctatcttttgctcaacaatattgtttaccaaattagaaaataagataatcttatccctgctgaattac----

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 3
TTGCAACAATAGCTTCTTCAGATGAGGCTGAACATGGCCTGGCATGTCCAAACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagca-gattacatcttatgttatctattacgcaatctatagaaaagtgtcttgataggactttgagaaacta--aacatcggttcaaaggcct--tcccttg
||||||||| ||| | | | ||||| ||||| ||||||||||||||||||| |||||||||||||||||  ||||| || ||||||||||| |||||||||| ||   ||    |  ||    ||  | || |    |||||      |       ||| || |||| |||  ||  |||   | ||       ||  |||||  
TTGCAACAACAGCATTTGCTGATGAAGCTGAGCATGGCCTGGCATGTCCAAGCTATCCATGGCCTCACAAGGGCATCCTTAGTTCATATGATCATGCTTCgtgagtttgacctgaaatttctctacattttcctt--tctattttcttgctcaacaatatga-tttgtgaagttagcaaccatgttttgtcaaactagtccct--

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G24620.2 (Glycine max), 5'ss of exon 3
TTGCAACAATAGCTTCTTCAGATGAGGCTGAACATGGCCTGGCATGTCCAAACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagc--agattacatcttatgttatctattacgcaatctatagaaaagtgtcttgataggactttgagaaactaaacatcggttcaaaggccttcccttg
|| ||||||| ||  |  | ||||| ||||| ||||||||||||||||||| |||||| ||||||||||  || ||||| ||||||||||| |||||||||||||    | ||  || ||   |    | |       |      || | | || |  ||  |  ||   ||| |  | |     ||  |  ||| |     
TTTCAACAATGGCAGCAGCTGATGAAGCTGAGCATGGCCTGGCATGTCCAAGCTATCCGTGGCCTCACAAAGGAATTCTTAGTTCATATGATCATGCTTCgtaagtttggcttgaattttccctatattgtcctatctttcgctcaacaatttcgtt-taccaagttagaaaattggatactcaatcttatccctgctgaa-

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 3
TTGCAACAATAGCTTCTTCAGATGAGGCTGAACATGGCCTGGCATGTCCAAACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagattacatcttatgttatctattacgcaatctatagaaaagtgtcttgataggac--tttgagaaactaaacatcg-gttcaa--aggccttcccttg
||||||||| ||| | | | ||||| ||||| ||||||||||||||||| | ||||||||||||||| |  ||||| || ||||||||||| |||||||||| ||    ||       |  || ||||        | | ||      |  ||  | |  |   |||| |||  ||   |    |||||   |  |    ||   
TTGCAACAACAGCATTTGCTGATGAAGCTGAGCATGGCCTGGCATGTCCTAGCTATCCATGGCCTCATAAGGGCATCCTTAGTTCATATGATCATGCTTCgtgagt---ttgacctgaaatttctctacattttcctttctatttttcttgctcaacaatatgatttgcgaagttagcaactatgttcagtcaaactagtccc--

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 2
TTGCAACAATAGCTTCTTCAGATGAGGCTGAACATGGCCTGGCATGTCCAAACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaag----cagattacatcttatgttatctattacgcaatctatagaaaagtgtcttgataggactttgagaaactaaacatcggttcaaaggcc-ttcccttg----------
|| | ||  | || ||| | ||||||||||||||||| ||||  ||||| ||||| || ||||| ||    ||||||||||| ||||||||||||||||||| ||    ||   ||||  | |  | ||| ||   | |||    | |  |  ||     |   | || |||||| |  | |  | || |  | |  ||   |||          
TTTCTACTGTTGCATCTGCTGATGAGGCTGAACATGGTCTGGAGTGTCCTAACTACCCTTGGCCACATGAGGGCATTCTCAGCTCATATGACCATGCTTCgtgagtgttcaagctacaattca-atcatc-atagtgaaattgcaacactaaagt-----tgaaaattagagaaatttgagactgctttactgacggttgatttgtaatgagcag

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:     CATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: CATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
EST: gi|349813644|gb|FQ413878.1|FQ413878
EST:     AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
EST: gi|351028222|gb|FQ426123.1|FQ426123
EST:     AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
EST: gi|110429073|gb|EC995560.1|EC995560
EST:     AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
EST: gi|351033244|gb|FQ462016.1|FQ462016
EST:     AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
EST: gi|18458621|gb|BM436899.1|BM436899
EST:     AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
EST: gi|349808524|gb|FQ405668.1|FQ405668
EST:     AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
EST: gi|351017876|gb|FQ436229.1|FQ436229
EST:     AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
EST: gi|349809896|gb|FQ398521.1|FQ398521
EST:     AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTC                         GATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC
genomic: AACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagat ... acaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAACAATAGCTTCTTCAGATGAGGCTGAACATGGCCTGGCATGTCCAAACTATCCATGGCCTCACAGCGGCATTCTCAGTTCATATGACCATGCTTCgtaagcagattacatcttatgttatctattacgcaatctatagaaaagtgtcttgataggactttgagaaactaaacatcggttcaaaggccttcccttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttccc