Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatcgtctatcatttggagacttgttcttagtttaacccactttcaacttctggaacacattatcaaattccctcctatctgatgtttttcttctttgttgatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGTCTAGCTTACCTTGGAGAAATTGGACAAGAAGCTTCATTAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g02910.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 9
gtcatcgtctatcatttggagacttgttcttagtttaacccactttcaacttctggaacacattatcaaattccctcctatctg---atgtttttcttctttgttgatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGTCTAGCTTACCTTGGAGAAATTGGACAAGAAGCTTCATTAAG
                  |     ||   ||  | |  |        |  ||    ||  |  | ||  ||    |   || |    |  |   |  |  ||  |  | ||||||||| |||| |||||||| || || ||||||||| || | |||||||||||| |||||| |||||| || |||||||||  | | || |||||
------------------gtagtatggctttcatgtgtcttttgaatagatttcaaaatgctatgtcttatgtgtttggatatacaaacatacatgcttcttaattgtggaacagATTCTAGCTATCCGTGCTCAAGTAGAGGAACTGGTTGTGGATGAAGAAAGTTTAGCTTTCCTTGGGGAGATTGGACAACGAACATCTTTAAG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 9
gtcatcgtctatcatttggagacttgttcttagtttaacccactttcaacttctggaacacattatcaaattccctcctatctgatgtttttcttctttgttgatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGTCTAGCTTACCTTGGAGAAATTGGACAAGAAGCTTCATTAAG
           |  | |||    |  |  ||  || ||     ||||||  | |  | ||   | |    ||      || |  |  |   |  |  ||  |  | | ||||||| |||| |||||||| || || ||||||||| || | |||||||||||| |||||| |||||| || ||||||||| || | || |||||
----------gtagtatggcc-ttcatctttctttcaaatagatttcaaaatgttaagcattatgt---gtttggatata-caaacatacatgcttcttaattgtgggacagATTCTAGCTATCCGTGCTCAAGTAGAGGAACTGGTTGTGGATGAAGAAAGTTTAGCTTTCCTTGGGGAGATTGGACAACAAACATCTTTAAG
















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|71873591|gb|DT022646.1|DT022646
EST:     GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|71878775|gb|DT027830.1|DT027830
EST:     GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|32246436|gb|CD712255.1|CD712255
EST:     GGTTGGTGATTGTACGGACTGAAACTTATGGTCCTGGTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|77579990|gb|DV218875.1|DV218875
EST:     GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|32246435|gb|CD712254.1|CD712254
EST:     GTTGGTGATTGTACGGACTGAAACTTAT-GTACCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GTTGGTGATTGTACGGACGGAAACTTATGGT-CCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|71880713|gb|DT029768.1|DT029768
EST:     GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|27586915|gb|CB009610.1|CB009610
EST:     GGTTGGTGATTGTACGGACTGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|71877702|gb|DT026757.1|DT026757
EST:     GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|77584731|gb|DV221439.1|DV221439
EST:     GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|71876313|gb|DT025368.1|DT025368
EST:     GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|71885171|gb|DT034226.1|DT034226
EST:     GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
EST: gi|110689388|gb|EE065570.1|EE065570
EST:     GATTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG                         ATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT
genomic: GGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAGgtcatcgtct ... gatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacattatcaaattccctcctatctgatgtttttcttctttgttgatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGTCTAGCTTACCTTGGAGAAATTGGACAAGAAGCTTCATTAAG
                                         tgttgat  putative branch site (score: 4)
                              tttttcttctttgttg  CT-rich tract
     ttatcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatcgtctatcatttggagacttgttcttagtttaacccactttcaacttctggaacacattatcaaattccctcctatctgatgtttttcttctttgttgatcgaacagATTTTAGCAATCCGTGCACAGGTGGAGGAACTGATTATAGATGAAGAAAGTCTAGCTTACCTTGGAGAAATTGGACAAGAAGCTTCATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC