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

gtgccctctcttctctaaattgcatcttaatttcatgtgaattctggagtcgtttcatttgcgtaattataataattatcattattattttaattttttcattaatcgatccattttacgtgaactcctctatgcaattctttgtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAG

Basic information

species Vitis vinifera
transcript Vv04s0008g05570.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g05570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 1
gtgccctctcttctctaaattgcatcttaatttcatgtgaattctggagtcgtttcatttgcgtaattataataattatcattattattttaattttttcattaatcgatccattttacgtgaactcctctatgcaattctttgtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAG
                               ||||  |       |||  | | |  ||| |||  ||   | | || |  | ||| ||   || |   ||   |||     |||||||   ||||       |||| | ||   |   |||||  |  | ||||| || ||||||||||| || ||||| ||| ||||||| ||||||| |||||| || ||| |||||
-------------------------------ttcacata-----cgga--catcttgttttcgttctttctacatttgttttcatttttcagatct---caggtatc-----attttact--aactttg----gcaacttttcaatcc-gcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCTGTGCAAATGTCATTACGCTCCTTCAG

upper sequence: Vv04s0008g05570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 1
gtgccctctcttctctaaattgcatcttaatttcatgtgaattctggagtcgtttcatttgcgtaattataataattatcattattattttaattttttcattaatcgatccattttacgtgaactcctctatgcaattctttgtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAG
                                        |     ||  |  |   |   |  ||  || ||        |||||  ||     ||| ||||    || ||  ||| | || |||  | |  | | ||||   |||  |||||  |  | ||||| || ||||||||||| || ||||| ||| ||||||||||||| | ||||||||||||| |||||
----------------------------------------accaaagaaccaat--gtccacagaaagatgatg-----tgttattgcttcg---tttccattttcagaacccatttgc-tgtactaattttggtacttctcaattt--gcagTGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTTGTGCGAATGTCATCACACTCCTTCAG

upper sequence: Vv04s0008g05570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 1
gtgccctctcttctctaaattgcatcttaatttcatgtgaattctggagtcgtttcatttgcgtaattataataattatcattattattttaattttttcattaatcgatccattttacgtgaactcctctatgcaattctttgtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAG
                                              ||| |  |   |   | ||   || ||   | |   |||| ||||   |||| ||||    |||||  |||  | | |||  | |  | ||||||   |||  ||||| ||  | ||||| || ||||||||||| |||||||| ||  | |||||||| |||| ||||||||| ||| |||||
--------------------------------------------atgagccaat--gtccacatagacatgatg--tcttgctattgttttg--ttttccattttcagatccgatttgtg-gtactaattttggtaattctcaattt--gcagTGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG

upper sequence: Vv04s0008g05570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S123_60V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgccctctcttctctaaattgcatcttaatttcatgtgaattctggagtcgtttcatttgcgtaattataataattatcattattattttaattttttcattaatcgatccattttacgtgaactcctctatgcaattctttgtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAG
                                          |   ||||       |   | ||||  || ||| |   |||  |    |   | ||  |||| |   | |||    |||| || ||   |      |         |||||||||||||||||| ||||||||||||||  | ||   |||| | || |||||||||| |||||||||| |  | |||
-----------------------------------------gttcagagttaccagctggacttaatctta-taagtggaattggttcagtctgtgttgtattagtaacttcata--gcgtggacgccctgagttggat---------tgcagTTCTATTGGTGATGTTCAACAAAGCAGCGTTGTCGAGTTATAAATTTCCTTGTGCAAATGTCATCACAGTAATGCAG

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|352768139|gb|FQ467278.1|FQ467278
EST:     CATGTCCAAGAGAGGAGCCTACGCTGCAATCTCTTACATGTCCTGCGCAG                         TTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTT
genomic: CATGTCCAAGAGAGGAGCCTACGCTGCAATCTCTTACATGTCCTGCGCAGgtgccctctc ... gtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaatcgatccattttacgtgaactcctctatgcaattctttgtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAG
 cattaat  putative branch site (score: 3)
                                       ttctttgtttttgc  putative PPT
                                     aattctttgttttt  TA-rich tract