Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtatgtaaattggttttgggattgctctatccatgttttgttgtagtttacttgatgtagaaaaagtgacttcattacattctaatgatggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCA

Basic information

species Vitis vinifera
transcript Vv17s0000g05880.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05880.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g16550.1 (Oryza sativa), 3'ss of exon 1
--gtgtatgtaaattggttt-tgggattgctctatccatgttttgttgtagtttacttgatgtagaaaaagtgacttcattacattctaatgatggtt-tgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCA
   | | |  | |  |  ||   | || |  || |  || ||||| | |  |  |    |||  ||   | |    |  |||  || |  | ||  || |  |||| |||||||| ||| |||||| ||||||||||||  | ||||| ||| |||||||||||||||||||  | |||||||||||||| || |||||||| |
tgatttgttgacacagacttactgtatggaactgtttatcttttggtctgatgaa----atgcggactgatttttatttttatttttttgtaatttttctatagGAAGTTCATGACTACCTGAAAAGCCTTTGTCCTGATCTCCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTA

upper sequence: Vv17s0000g05880.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G068489_T01 (Zea mays), 3'ss of exon 1
gtgtatgtaaattggttttgggattgctctatccatgttttgt-----tgtagtttacttgatgtagaaaaagtgacttcattacattctaatgatggtt-tgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCA
    |||  |     ||||   |||||   ||  ||| |||||        ||| |  ||| | |    |||  ||    | || ||||| || ||     || |||| || ||||| ||| |||||| |||||| |||||  | ||||||||| |||||||| ||||||||||  | || ||||||||||| || |||||||| |
----atggtatcccatttttctattgcag-attgatggtttgtatgaactgagtgtttttgttctgatgaaatagagagtaata-attctcataatttcaatgtagGAAGTCCATGACTACCTGAAAAGCCTTTGCCCTGATCTCCATATTACCAGAGGTGAACATGATGAGGATGCTCGATACCCAGAGACTAAGACACTTACAA

upper sequence: Vv17s0000g05880.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G109315_T02 (Zea mays), 3'ss of exon 1
--gtgtatgtaaattggttt--tgggattgctctatccatgttttgttgtagtttacttgatgtagaaaaagtgacttcattacattctaatgatggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCA
      | |    |||| |   |||||  |   | |      | ||      ||  | |  ||  |||| |  ||||  | || ||| | || ||  |||| |||| |||||||| ||| |||||| |||||| |||||  | || |||||  ||||||||||||||||| |  | || ||||||||||| || |||||||| |
ggacccaggacctttggctcagtgggaaaggcttcttaccactatgccaggtttgtccttctgatgaaatacagact--aata-attttcataatt-tttgtagGAAGTTCATGACTACCTGAAAAGCCTTTGCCCTGATCTCCACATTACTGGAGGTGAATATGATGAGTATGCTCGATACCCAGAGACTAAGACACTTACAA

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|32267465|gb|CD716428.1|CD716428
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTGCCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|71890537|gb|DT039592.1|DT039592
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|32272444|gb|CD721603.1|CD721603
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTGCCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|32247405|gb|CD713224.1|CD713224
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTGCCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|110732723|gb|EE108257.1|EE108257
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|32265181|gb|CD716770.1|CD716770
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTGCCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|110732750|gb|EE108311.1|EE108311
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|34320397|gb|CF373151.1|CF373151
EST:     TTCCTGGCAAGATNCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|110383433|gb|EC947806.1|EC947806
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|33401447|gb|CF207074.1|CF207074
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
EST: gi|71890549|gb|DT039604.1|DT039604
EST:     TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAA                         GAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA
genomic: TTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctt ... tggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttacttgatgtagaaaaagtgacttcattacattctaatgatggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCA
                                    ttctaat  putative branch site (score: 2)
              tagaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtatgtaaattggttttgggattgctctatccatgttttgttgtagtttacttgatgtagaaaaagtgacttcattacattctaatgatggtttgcagGAGGTTCATGATTACTTGAAAACCCTTTGTCCTGACATGCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
gtgtatg
- - - - - - - -ttttggg
- - - - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa