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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtatttttcctttacttaggatgaggtaactgtctaggaaaaatgaatctagctgtatatgcatgcatgcacgactaagcatataaaggggaatgt...

Basic information

species Vitis vinifera
transcript Vv10s0003g01700.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 3
CAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtatttttcctt------tacttaggatgaggtaactgtctaggaaaaatgaatctagctgtatatgcatgcatgcacgactaagcatataaaggggaatgt
| || || |||||||| || || ||||| || |||||||||||||| ||  | ||| ||||||||||||| ||||| || |||||||| ||||| || |||||||  |||| ||        |  |||  || |  ||  | |  | ||    || ||        |     |    |   |   | |   |  || ||       
CGATTTACTTGGAGGCAGTGGCAATTCTCCCTCAGTTAGTTTTGCTGCAGAGAAGTAGAAATGTGGACAACTTGACTGGACAATATGTATTCTTCCTAGGgtatgagttttaccacacaagctttttaccataacatatttatacatgattcctgtattacaagagaatgaaacatgtttgcttttcatgcttcaacggc------

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G101413_T01 (Zea mays), 5'ss of exon 3
CAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtatttttcctttacttaggatgaggtaactgtctaggaaaaatgaatctagctgtatatgcatgcatgcacgactaagcatataaaggggaatgt----
|||| ||||||||||| || || ||||| || || ||||| ||||||||  | ||  |||||||||| || || || || |||||||||||||| |||||||| || |||| | | |  |  | |    |    | |   | | | ||   |   |   |  | || ||| |  |   |||  |   ||||||   ||      
CAATCTATTTGGAGGCAGTGGCTATTCTCCCACAATTAGTGTTGCTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttttacttcttgtcggcaatttgctgtttttctgaacacatctgtt--gtattcaaagcctgc-tatagtgctatccg-gtaaaggtccattactcc

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G12570.1 (Glycine max), 5'ss of exon 3
CAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtatttttccttta--cttaggatgaggtaactgtctaggaaaaatgaat-ctagctgtatatgcatgcatgcacgactaagcatataaaggggaatgt-
||||||| |||||||| ||||| ||  | || ||||| |||||| | ||| | ||||||||||||||||||||||| | ||||||||| |||||||||||||||| |   |||  ||    |     |     | ||| ||        ||  | ||  || ||| | | |   |   |   | | ||| ||   |  | |   
CAATATACTTGGAGGCAGTTGCAATATTACCTCAGTTGGTTTTGTTGCAAAGAAGTGGAAATGTGGACAATTTGACTGTGCAATATGTATTCTTTCTTGGgtatgcacacttctgttgagttctcttttgaagatctgcctttatgttttggttgcttactctatgttcttttttatgc---tgatcat-tagcagatagtcct

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G29410.1 (Glycine max), 5'ss of exon 3
CAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgta--tttttcctttacttaggatgaggtaactgtctaggaaaaatgaat--ctagctgtatatgcatgcatgcacgactaagcatataaaggggaatgt
||||||| |||||||| ||||| ||  | |||||||| |||||| | ||| | ||||||||||||||||||||||| ||||||||  | |||||||||||||||| |   ||||  |    |     | |   | ||| ||        ||  |   ||  ||  ||     | ||   | | | |  ||   |     |    
CAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAATACATATTCTTTCTTGGgtatgcacgcttttgttgagttctcttttaaagatctgcctttatgttttggttgcttacttgcttacaatggtatcttctagtgacaatggtatactaa----

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G29330.1 (Arabidopsis thaliana), 5'ss of exon 3
CAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtatttttc-ctttacttagg-atgaggtaactgtctaggaaaaatgaatctagctgtatatgcatgcatgcacgactaagcatataaaggggaatgt
| || || || ||||| ||||| || ||||||||||| ||| |||| ||| | ||||| ||||| ||||||||||| |||||||||||| ||||||| ||||| ||| || |  |   || || |  |  | | |||   |    |           | ||  | ||  |  |     |  | | | |||| |    | || 
CTATCTACTTAGAGGCAGTTGCTATCCTTCCCCAGTTGGTTCTGCTACAAAGAAGTGGGAATGTCGACAATTTGACTGGGCAATATGTTGTCTTTCTCGGgtacgtaattctaaccagacatatgcgtttgctcacttgatctccactggcttctctgttgggtttgtttttagaattggtttatcttatatatat-actg-

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|352787179|gb|FQ477799.1|FQ477799
EST:     CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGG                         GGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTACTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
EST: gi|30298685|gb|CB975479.1|CB975479
EST:     CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGG                         GGCTTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
EST: gi|110720994|gb|EE097488.1|EE097488
EST:     CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGG                         GGCCTATCGAGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
EST: gi|110686747|gb|EE064739.1|EE064739
EST:     CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGG                         GGCCTATCGAGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
EST: gi|110703644|gb|EE080669.1|EE080669
EST:     CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGG                         GGCCTATCGAGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
EST: gi|30298746|gb|CB975540.1|CB975540
EST:     CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGG                         GGCTTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
EST: gi|110688848|gb|EE067872.1|EE067872
EST:     CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGG                         GGCCTATCGAGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
EST: gi|110687293|gb|EE064579.1|EE064579
EST:     CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGG                         GGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
EST: gi|351040756|gb|FQ438300.1|FQ438300
EST:     CGCACTGGAAATGTGGACAATTTGACGGGGCAATATGNNNNNNNNCTTGG                         GGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA
genomic: CGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtattt ... caatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAATATGTTTTCTTTCTTGGgtatgtatttttcctttacttaggatgaggtaactgtctaggaaaaatgaatctagctgtatatgcatgcatgcacgactaagcatataaaggggaatgt

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaggtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggaat