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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag

Basic information

species Vitis vinifera
transcript Vv08s0007g07460.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 2
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttct--ccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag
 ||||||||||| || || ||  | || || ||||||||||||||||||||| |||| || ||||||||||||| ||| ||| | || ||||||||||||||| ||  || | |    | |       || ||   | ||       |   ||  |||  |   || |  | |||||   |  |  |     |  |   |||
ATCTTTTGCTGGTGAACTGCTTGAGAAGGCCGAGGAGCTTATCAGGATGGGGTTGCATCCAAGTGAGATCATCATTGGCTACACCAAGGCCATTAATAAGgttacttaccctcccgattgagctggccttatattgattaaaaaaacctgttgcctga--tggcaggctagttattcatgcatttgcatctgcaatgcgcag

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G381744_T01 (Zea mays), 5'ss of exon 2
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctgg-atgaatttctagacatgctattctgactctctctctctctgtcttcag
 || |||||||| || || ||  | || ||||||||||| |||||||||||  |||| |||||||||||||||| ||| ||| | |||||||| || |||||  | ||   |   |  |       |  |     ||  | | |  |  ||  ||| | |   | |   | |  | ||  |   |     |  || | |||
ATCGTTTGCTGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCGAGTGAGATCATCATTGGCTACACCAAAGCCATCAACAAGgtgacacccctccccccgac------tcctgtaggcttctgtacaacattgacatgcagtctgatagcaggtcctttg--tgctttgtatttggtatgcag

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 2
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgt----ttctccatg---cttgctaatgctttgttttaacaactagtcttctccc---ctggatgaatttctagacatgctattctgactctctctctctctg----tcttcag---
 || ||||| || || || ||  | || ||||||||||| |||||||||||  |||| || ||||||||||||| ||| ||| | |||||||| || |||||    | | || ||   || |||  ||   | ||  |||    |||||  |  |   ||   ||   || |     || ||| | |||  |     |||  |    ||||      
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgccccctgactctggcttttgtaatattgaaacgtgcagtctgatagcaggctctttgtgcttttgtctttggtatgcagacaattgagatcttggaggatcttgttgag

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 2
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag
 || ||||| || || || ||  | || ||||||||||| |||||||||||  |||| || ||||||||||||| ||| ||| | |||||||| || |||||  ||   |||   || |  ||   ||||      || | ||    | || |    | |     || ||| ||      || |     |  || | |||
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgact---tgccccctgactctggcttttg-----taatattgaaacgtgca---gtctgatagcaggctcttt--gtgcttttgtctttggtatgcag

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 2
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag
||| |||||||| || ||||| ||   ||||||||| ||||||||||||||  |||| ||||| |||||||||||||||||| | ||||| || || |||||||      |     || |  ||  |||| | |  |  | ||  |  ||   |    ||||| |  |  | || ||  ||                   
TTCATTTGCTGGGGAACTCCTGCAGGGTGCTGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCGATCAACAAGgttttgatgagagccttagtcattcatttttaaatgtcatattg-ctgctctctcttcttcta-atgtattgttttgtgtcag-----------------

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag
||| |||||||| |||||||| ||   ||| ||||| ||||||||||||||  |||| ||||| |||||||||||||||||| | ||||| || || ||||||| | ||   ||  | |||    |  |||   |   |||||      |      ||| ||   |   ||      | | |||   | | |   |||||
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttt--tgatgaaa-gccttagtgatctgtctttaaatgt---catattgctgctctctctccctctaatttcttgttttgt---ttcag

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag
 || |||||||| || || || ||||| ||||||||||||||||||||||| || || |||||||||||||| ||||||||  | |||||  | |  ||||||  |  || | ||  | | || | || |       | | |  |   || || | ||||   || ||||||||  |  | |   |    | |       
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctga-attactgttttgtgcttttcaatttgtttgtcttga-gtatttgacga-atgctatt--ggattttgattatgcag-------

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|34544165|gb|CF512397.1|CF512397
EST:     GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAG                         ACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
genomic: GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccat ... ctgtcttcagACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
EST: gi|71859802|gb|DT008857.1|DT008857
EST:     GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAG                         ACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
genomic: GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccat ... ctgtcttcagACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
EST: gi|351014857|gb|FQ438057.1|FQ438057
EST:     GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAG                         ACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
genomic: GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccat ... ctgtcttcagACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
EST: gi|110720434|gb|EE096355.1|EE096355
EST:     GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAG                         ACTGTTGAAATTATGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
genomic: GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccat ... ctgtcttcagACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
EST: gi|110700665|gb|EE077518.1|EE077518
EST:     GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAG                         ACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT
genomic: GGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccat ... ctgtcttcagACTGTTGAAATTTTGGAAGAATTGGTTGAAAAAGGTTCTGAAAAAATGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA