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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttccccaattggttatggtttctttcagttttgaaagcaaaattcataagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
---------------------------tttttccccaattggttatggtttctttcagttttgaaagcaaaattcataagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA
                             |     |    |||  ||||    ||   | |  |       | || |  | |  | |        | | |    ||||       || | | |  ||||  ||||||||| ||| ||||| ||||||   |||||||| || || || |||||||||||||| |||||||| ||| |||||||||| |||||  | |
gtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactc-tgtgagcttcaaaaaaataaaaatgcctaatgacc---ctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
tttttccccaattggttatggtttctttcagttttgaaagcaaaattca-taagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA
  | |  |    ||   | | |       | |       |   ||     |   || ||||     || |  |||    ||   |   |   || ||| ||||  ||||||| | ||| ||||||||||||   |||||||||||||| || |||||||| || || || ||||| ||| ||||||| || |||||  | |
-gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgata--tacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 9
tttttccccaattggttatggtttctttcagttttgaaagcaaa-attcataagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA
|  ||      | |  |  || |  |||   |||     | ||  |||   ||||    || |  | | |  || || | | | ||||| ||||||||||||||||||||||||||||||||| ||| ||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||||||||| |||
tgctttgagggtcgagttaggctcatttttttttcatttgtaaccattttgaagttgggtaacctgaaaaagttctttatttgctgaat-ccatcctacagGTGTTGTATGACTATGAAGACAGAATAAATCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCTGGCTTAGCAGTTGCACTGA

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA14G36280.2 (Glycine max), 3'ss of exon 9
tttttccccaattggttatggtttctttcagttttgaaagcaa--aattcataagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA
|  ||      |||  |  || |  |||   |||     | ||  | |||| |  ||  | | |||  | | ||| || | |   ||||| ||||| ||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||| |||
tgctttgagggttgagttaggctcattttgttttcatttgtaaccatttcaaagttgggtaacctgaaaaa-attctttattttctgaat-ccatcttacagGTGTTGTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGA

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 9
tttttccccaattggttatggtttctttcagttttgaaagcaaaattcataagtgaatt---atctggcacacatttttcaatggttg-aattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA
             |   ||  ||  ||||  | ||| |    || |   ||| | | ||    |     ||  |||||     | ||| || |  | |  | ||||  ||||||||||||| |||| ||| ||||| ||||| ||||||||||| |||||||| ||||| ||||| |||||  | ||  ||||||||||  |||
-------------gtgaatttttcgtttctatattgtatatgaa-tgagtaaataacttccagttactgactaattttatgtcgtttgtaactttacctgatagGTCATGTATGACTATGAGGACAGAATTAATCAAGCTGTTTTTCCTGGACTGCAAGGTGGTCCACATAATCACACTATAACGGGTCTAGCAGTTGCTCTGA

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|161709499|gb|FC058863.1|FC058863
EST:     TGATATTCTTCAGGAAGGGGGTTAAAGAGATCAACAAACAAGGGAAAGAA                         GTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATATTCTTCAGGAAGGGGGTTAAAGAGATCAACAAACAAGGGAAAGAAgtgagtcttg ... catcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|110383662|gb|EC948045.1|EC948045
EST:     TGATATTCTTCAGGAAGGGGGTTAAAGAGATCAACAAACAAGGGAAAGAA                         GTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATATTCTTCAGGAAGGGGGTTAAAGAGATCAACAAACAAGGGAAAGAAgtgagtcttg ... catcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|110361032|gb|EC924482.1|EC924482
EST:     AGAGATCAACAAACAAGGGAAAGAA                         GTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: AGAGATCAACAAACAAGGGAAAGAAgtgagtcttg ... catcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|161777280|gb|FC072695.1|FC072695
EST:     TGATATTCTTCAGGAAGGGGGTTAAAGAGATCAACAAACAAGGGAAAGAA                         GTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATATTCTTCAGGAAGGGGGTTAAAGAGATCAACAAACAAGGGAAAGAAgtgagtcttg ... catcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|351022221|gb|FQ438806.1|FQ438806
EST:     CAACAAACAAGGGAAAGAA                         GTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: CAACAAACAAGGGAAAGAAgtgagtcttg ... catcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|351043008|gb|FQ434449.1|FQ434449
EST:     CAAACAAGGGAAAGAA                         GTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: CAAACAAGGGAAAGAAgtgagtcttg ... catcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcataagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA
                                          ttccatcct  CT-rich tract
                         atttttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttccccaattggttatggtttctttcagttttgaaagcaaaattcataagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- tttcccc
- - - - - - - - - - - - - - - - - - aaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttga