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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataattttttttctttttcatcaatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC

Basic information

species Vitis vinifera
transcript Vv00s0194g00070.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g19444.2 (Oryza sativa), 3'ss of exon 4
actaaaataagggtaggatttttatggaatttgattagaatgaaaatt--ttcataactaaaaaataattttttttctttttcatcaatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC
  |   |      |     |   |||  || |   ||| ||   ||||   || |   | | |  ||  |  || ||||||          ||  ||| ||||||||| |||||||| || ||||| |||||||| || ||||||||||| || ||  | || ||||| || |||||||||||||| || || || || |||
-atgtcagtccactgatgctaacatgctatatttctagcataccaattgcctcctttttgacagctagctgattatcttttctcatggcttctcttga-cagATTTGACAAGAAAATCAGGTATGCATCTCGCAAGGCTAGGGCAGATGTGAGAAAAAGAGTCAAGGGCCGGTTTGTTAAGGCTGGTGAAGCATACGACTAC

upper sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g49230.2 (Oryza sativa), 3'ss of exon 6
actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataattttttttcttt-ttcat-caatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC
  | | | | | | | | ||  |       |  ||   | |  |  ||||  | |  | ||  || | | |   |||| ||||   | |  ||| | ||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| || ||  | || || || || ||||| ||||||||||| || ||||| |||
--ttagacatgtggatgcttgctcctagtgtgaatgctactttatgtttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC

upper sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G167560_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------actaaaataagggtaggatttt-------tatggaatttgattagaatgaaa-attttcataactaaaa--aataattt-tttttctttttcatcaatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC
                                                                         | |||| | |  |   |  ||       | | |  | |  ||   || |   |||||| |  |  ||     | |||    |||| ||||||  |||   |  |  |||| ||||| ||||| || |||||||| |||||||| || |||||||| || |||||| | || ||||| || ||| | ||||||||||| || ||||| || 
gtaagcacgtttaaatgtctgcttgaggttgttctgcgcttaacattcatagatcgtggctatctttttaaggcaaaaaaatgtctccaaccttctgtgtctcttgtttctagtttcgataatgcattttccttgcagaagtcgctgattcacctttccttttcacgaat--ttggtcgacagGTTTGACAAGAAGATCAGATATGCTTCTCGCAAGGCTAGGGCAGACGTGAGGAAGAGGGTCAAGGGACGGTTTATAAAGGCTGGCGAAGCGTATGACTAT

upper sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G38870.1 (Glycine max), 3'ss of exon 5
actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataattttttttctttttcatcaat----gacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC
    || ||         | ||||| | || |||||    |  ||||||| | |||| |         ||| |  |||  |||||||    |   | | |  || || ||||||||| ||||||||||||||||||| || ||||| |||||||| |||||||||||||| |||||||| || ||||| ||||  ||||| || 
---taactacttactaattatttattggatatgatttatttctaaattttaa-aacttatttgctccgtttgtgatttaacatcaattgtggttatcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAGAAAGCGTGTGAAGGGCCGATTTGTCAAAGCTGGTGATGTCTATGACTAT

upper sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G36930.2 (Glycine max), 3'ss of exon 5
actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataattttttttctttttcatcaat----gacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC
   || ||||      | |  |||| | || ||||| |  |  ||||||| |||||| |       |  |  |  |||  |||||||    |   | | |  || || ||||||||| |||| |||||||||||||| || ||||| |||||||| |||||||||||||| |||||||| || || || ||||  ||||| || 
---aatataactacttgctaattattggatatgatttgtttctaaatttt-ataacttatttgctttgctggtgatttaacatcaattgtggttatcttattagGTTCGAGAAGAAAGTAAGGTATGCCTCTCGCAAGGCTAGGGCTGATGTCAGAAAGCGTGTGAAGGGTCGATTTGTCAAAGCCGGTGATGTCTATGACTAT

upper sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G07650.2 (Arabidopsis thaliana), 3'ss of exon 4
actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataatttttttt------ctttttcatcaatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC
           |  || | |  | || || |  |     ||||  ||  |   |   |    |  |||||  |       || |  | ||  |    |   ||||| ||||| |||| | | || ||||| || ||||||||||| || ||||| ||   |||||| |||||||||||||| || ||||| || ||||||||||||
-----------gtaagtagtagtctgaaactgcaaatacatgagcatcattgaagtgagtgcaggattttcctaatgtgactctggcttcttttttctggaaacagGTTTGATAAGAGAGTGAGGTATGCTTCCCGCAAAGCAAGAGCTGATGTGAGACGGCGTGTAAAGGGGCGATTTGTCAAAGCTGGTGAAGCTTATGATTAC

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|30303708|gb|CB980502.1|CB980502
EST:     AACA-GGATAGTGCTGTCTTGCGTTACAAGGAAAAGAAAAAGGCACGAAA                         ATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAG
genomic: AACAGGGATAGTGCTGTCTTGCGTTACAAGGAAAAGAAAAAGGCACGAAAgtaagtacac ... ttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAG
EST: gi|110361370|gb|EC924837.1|EC924837
EST:     AACAGGGATAGTGCTGTCTTGCGTTACAAGGAAAAGAAAAAGGCACGAAA                         ATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAG
genomic: AACAGGGATAGTGCTGTCTTGCGTTACAAGGAAAAGAAAAAGGCACGAAAgtaagtacac ... ttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttcataactaaaaaataattttttttctttttcatcaatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC
        aactaaa  putative branch site (score: 2)
      ataactaaaaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataattttttttctttttcatcaatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC

- -aaaataa
- - - - - gggtagg
- - - - - - - - - - - - - - - - - - - -atgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa