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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgattttgtttcttcttgtgtaaatagatatacaactttacacttctggttggatgtcattctctaattttccattatttgttcttttaattggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG

Basic information

species Vitis vinifera
transcript Vv18s0001g00480.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 7
---------------------gcttgattttg---tttcttcttgtgtaaatagatataca------actttacacttctggttg-gatgtcattctctaattttccattatttgttcttt--taattggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG
                       ||| | |||   | |||| || |   ||    ||||         || |    |  || ||| | |||||     |  ||||| | |  ||| | |     | |  |||||| ||||||||||||||  | ||||||||| | ||||  ||||||||||| ||||| ||||| ||||||||||||||
gtattcacagggttgagtggaagttggtgttgaaatatcttgttattgcaactactatatctgggatgctgtctgatgatgtttgtgttgtcacatgatgcttttctaatgattgatatgcaccactgtgcagGGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 3'ss of exon 7
------------------------------------------------------gcttgattt-tgtttcttcttgtgtaa---atagatatacaacttt--acacttctggttggat-gtcattct--------ctaattttccattatttgttcttttaat---tggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG
                                                        ||||||| ||  | ||  |   ||       | ||||   | ||  | |||| |  ||  |   |||||          |  ||| |   || | ||| ||  || |   | ||||||||| || ||||||||  | ||||||||| |||||||  ||||||| || || || ||||| ||||||||||||||
gtactgaaattgttaatgctttatactatatatttgcagttagttgttttgaacttttgatttgtgactgttactacatattctgccgctatattgccttaaatacttttcattataccatcatttaagtcactgcagattctgatttgtgtgtgctactactgaattgcagGGCAGTACCAACTTGGAAGCAATTCAAATTCTTAAGAAAACTGGAGGGTCTCTAAAGGACTCCTTTTTGGATGAAGG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------gcttgattttgtttcttcttgtgtaaatagatatacaactttacacttctggttggatgtcattctctaattttccattatttgt-------tcttttaat--tggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG
                                                             |  | |||||   ||||               ||||  | |  ||  || |    | ||| ||||  |  | ||  | ||||  |       | | | |||  |||||||| ||||| |||||||| |||||||||||| | ||||| ||||||||||| ||||| || ||||||||||| |||||
gtatacaaatagcttaattaaagttggttatcatttacattaaactttgatatgtttatctgtataattttaactcttgaaaaagtgtggttcatacttcatagcaactcagtcgtgttgttattcgatggtgttatagtattgatcggtttctatctgaatggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTCAAGGATTCATTTTTGGACGAAGG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 15
gcttgattttgtttcttcttgtgtaaatagatatacaactttacacttct-ggttg-gatgtcattctctaattttccattatttgttc-ttttaat--------tggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG
           ||    ||||   || ||  | |   |||| | ||| ||  ||   | ||| ||||  |  | ||    ||||| ||  |||  ||        |||||||| ||||| |||||||| |||||||||||| | ||||| ||||||||||| || || || || |||||||| |||||
-----------ttaagccttgaaaaagtatgtcttatacttcatactactcagtcatgttgttattcgatggtgttatggtatttattggtttcgatctgaatggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG

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|352769329|gb|FQ471478.1|FQ471478
EST:     ACAAGGAACATTTTGCAAAACTGGCAGTAGATGCTGTTATGAGACTGAAG                         GGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCA
genomic: ACAAGGAACATTTTGCAAAACTGGCAGTAGATGCTGTTATGAGACTGAAGgtgagtaatg ... taattggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCA
EST: gi|352773730|gb|FQ472512.1|FQ472512
EST:     ACAAGGAACATTTTGCAAAACTGGCAGTAGATGCTGTTATGAGACTGAAG                         GGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCA
genomic: ACAAGGAACATTTTGCAAAACTGGCAGTAGATGCTGTTATGAGACTGAAGgtgagtaatg ... taattggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCA
EST: gi|352777695|gb|FQ466748.1|FQ466748
EST:     ACAAGGAACATTTTGCAAAACTGGCAGTAGATGCTGTTATGAGACTGAAG                         GGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCA
genomic: ACAAGGAACATTTTGCAAAACTGGCAGTAGATGCTGTTATGAGACTGAAGgtgagtaatg ... taattggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCA
EST: gi|352781730|gb|FQ469028.1|FQ469028
EST:     ACAAGGAACATTTTGCAAAACTGGCAGTAGATGCTGTTATGAGACTGAAG                         GGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCA
genomic: ACAAGGAACATTTTGCAAAACTGGCAGTAGATGCTGTTATGAGACTGAAGgtgagtaatg ... taattggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctggttggatgtcattctctaattttccattatttgttcttttaattggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG
                                          ttttaat  putative branch site (score: 3)
                         ttttccattatttgtt  CT-rich tract
                      taattttccattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgattttgtttcttcttgtgtaaatagatatacaactttacacttctggttggatgtcattctctaattttccattatttgttcttttaattggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - cttcttg
- - - - - - - - - - - - aaataga
- - - - - - - - - - - - - - - - - - - - - - - - -tggttgg