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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttattataagttaaagaaaatgaaacaacccttctataatgaattgatacttaatttctctttgctttctattgacacatatttgaatttcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACTGATTATACTGCCGATGAG

Basic information

species Vitis vinifera
transcript Vv14s0066g02630.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G38670.1 (Glycine max), 3'ss of exon 1
cttattataagttaaagaaaatgaaacaacccttctataatgaattgatacttaatttctctttgctttctattgacacatatttgaatttcatgaat-agGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACTGATTATACTGCCGATGAG
          || |       |  | |  |  | || | |    |  ||   || |||||  ||  ||| ||  || | || |||   |||| |   | |||| |||||||||||||| || || |||||||||||||||  ||| ||||||||||||||||| ||||||
----------gtaatctcttttatatccgcattgctgttacatttacatgtctattttcttctt--tttataa-gaaaaatgtttttttttcttctttcagGTGTTTACTTGGTATGGTGCAACCATTGAAATGGATGGTGCTACTGAAACTGATTATACTGCAGATGAG

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G07820.1 (Glycine max), 3'ss of exon 2
cttattataagttaaagaaaatgaaacaacccttctataatgaattgatacttaatttctctttgctttctattgacacatatttgaatttcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACTGATTATACTGCCGATGAG
       |||  |        |  | |  |  || | | |    |  ||   || |||||  ||  ||| ||  || | || |||   |||      ||||| |||||||||||||| || || |||||||||||||||  ||| ||||||||||||||||| |||| |
------gtaatctctttt---tatatccgcatttttgttacatttacatgtctattttcttctt--tttataa-gaaaaatgtttttttttatcttttagGTGTTTACTTGGTATGGTGCAACCATTGAAATGGATGGTGCTACTGAAACTGATTATACTGCTGATGTG

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G43930.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------cttattat--aagttaaagaaaatgaaacaacccttctataatga-attgatacttaatttctctttgctttctattgacacatat-ttgaatttcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACTGATTATACTGCCGATGAG
                                                                   | || ||  ||   |    | ||    |||||    | |  | | ||| | |      |||| ||| |||| |||    | ||||  |   |||       |||| |||||||||||||| || || ||||||||||||||   ||| ||||||||||||||||| ||||||
gtaaattcttttataaccgcattgctgtttttttttttctttttctttcccctctccccttatcccttaatcatccaacccaccttatatctcccaaccgcattgttgttacatttacatgcctgttcttttttctttttataagaaaatatgctctttttttcccccagGTGTTTACTTGGTATGGTGCAACCATTGAAATGGATGGCGCTACTGAAACTGATTATACTGCAGATGAG

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G04680.1 (Arabidopsis thaliana), 3'ss of exon 2
cttattataagttaaagaaaatga-aacaacccttctataatg---aattgatacttaatttctctttgctttctattgacacatatttgaatttcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACTGATTATACTGCCGATGAG
 || || |   ||        ||  ||  |    | || | |    ||| |   ||      | |  ||||| | ||         |||  |||  ||    ||||||| |||||||||||||| |||||||| ||||||||| | || |||||||| ||||| || ||||||
-ttcttttctatttttccttctgctaatgatttatgtaaagttcataatcggagctctgaaacaccgtgcttaccatct-tgtgccttttgatt--attgtcagGTTTTCACTTGGTATGGAGCGACAATTGAGATGGATGGTGTCACGGAAACTGACTATACAGCAGATGAG

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|351053969|gb|FQ441735.1|FQ441735
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|351048068|gb|FQ441240.1|FQ441240
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|351037774|gb|FQ464215.1|FQ464215
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|22013971|gb|BQ799005.1|BQ799005
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCT                         GTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTgtgagtactg ... tcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT
EST: gi|71862039|gb|DT011094.1|DT011094
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCT                         GTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTgtgagtactg ... tcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT
EST: gi|352791526|gb|FQ481105.1|FQ481105
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|351044652|gb|FQ443183.1|FQ443183
EST:     CCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCCGTGAGTACT                         GTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAAC
genomic: CCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT---C----G--CTgtgagtactg ... tcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAAC
EST: gi|351053260|gb|FQ459128.1|FQ459128
EST:     AGATTCCTCCCGAAACCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|161715992|gb|FC068763.1|FC068763
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCT                         GTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTgtgagtactg ... tcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT
EST: gi|110422874|gb|EC989207.1|EC989207
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCT                         GTTTTTACTTGGTATGGAGCCACAATTGAAATGGAGGGTATTACAGAAACT
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTgtgagtactg ... tcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT
EST: gi|352789973|gb|FQ479583.1|FQ479583
EST:     CCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGTTGTGAGTACT                         GTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAAC
genomic: CCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTC-------G--CTgtgagtactg ... tcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAAC
EST: gi|351046157|gb|FQ442535.1|FQ442535
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|351037634|gb|FQ462618.1|FQ462618
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|351039234|gb|FQ457909.1|FQ457909
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|351042381|gb|FQ442848.1|FQ442848
EST:     CCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCCGTGAGTACT                         GTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAAC
genomic: CCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT---C----G--CTgtgagtactg ... tcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAAC
EST: gi|351056907|gb|FQ443534.1|FQ443534
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTGTGAGTACT                 
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTT--C-----G--CTgtgagtactg ... tc
EST: gi|110731309|gb|EE105610.1|EE105610
EST:     AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCT                         GTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT
genomic: AGATTCCTCCCGAAATCTGGCTCTCCTTCCCTCCTAGACTCAAGTTCGCTgtgagtactg ... tcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatacttaatttctctttgctttctattgacacatatttgaatttcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACTGATTATACTGCCGATGAG
                         tattgac  putative branch site (score: 2)
                                  atatttgaatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttattataagttaaagaaaatgaaacaacccttctataatgaattgatacttaatttctctttgctttctattgacacatatttgaatttcatgaatagGTTTTTACTTGGTATGGAGCCACAATTGAAATGGATGGTATTACAGAAACTGATTATACTGCCGATGAG

- - - - - - - aagaaaa
- - - - - - - - - - - gaaacaa
- - - - - - - - - - - - - - -cccttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacata