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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtttaagaactcatggtgctcatttgacaaaaatgttatgaattattttattaatcctatctcacctaatattttggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA

Basic information

species Vitis vinifera
transcript Vv07s0005g02620.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 4
attgtttaagaactcatggtgctcatttgacaaaaatgttatgaattattttattaatcctatctcacctaatattttggtaatgttgactttttcct--agGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
||||| | || || | | | || ||| | | || | | | | | || | || | | | || || | |||| || ||||| || ||||| ||| |||| ||| |||||| ||||| || || ||||| ||||||||||||||||||||||| || | || || ||||
tctgttttgtttgttataaa--ctgttgcatacacattttacttttaggctatttgttggaacttgatacagtaacatagtcttttgtaattcatcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCAATCCGTCCTACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 4
-attgtttaagaactcatggtgctcatttgacaaaaatgtta--tgaat-tattttattaatcctatctcacctaatattttggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
| | | | || || |||| | ||| | ||||| | || ||| | || || | | ||||| || || | |||| |||||||| || |||||||| |||| || |||||| || ||||| || || || ||||||||||||||||||||||| || | || || ||||
gagttgcagacaggcaatagt-ttcatgaaatttgtttgtcaattgaatatcttccattgctactcgctttatgcaaaaaagagtaatatt---cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 5
attgtttaagaactcatggtgctcatttgacaaaaatgttatgaattattttattaatcctatctcacc--taatattt---tggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
|||| | || | |||| | | | | || ||| || ||| | | | || || || || | | | ||| |||| |||||||| ||||| ||||| |||| || || ||| | ||||||||||||||||| || ||||| ||||||||||||||||| || ||||||||||
---gttttatgtgatggaatggttattttttatgatt--tgcagtttctttccagaaggatattttaacattagtacttgtctgattgtcctacttttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCTATTCGTCCTACTAGTGAAACTGTCATGTATCCCTACTACTCTAAGTGGA

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 5
attgtttaagaactcatggtgc-tcatttgacaaaaatgttatgaa--ttattttattaatcctatctcacctaatattttggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
|||| | | || | | ||||| | | ||| |||||||| | | | || | | || | | || ||| |||| |||||||| ||||| ||||| |||| || || ||| | ||||| ||||||||||| || ||||| || || ||||||||||| || ||||||||||
--tgttggaatggttattttttatgatttgctgtttctttccagaaggacattttattttgaaaagattag-tacttgtctgattgtcttacttttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCCGAATTAGAAATTCCTATAGCTATTCGTCCTACTAGTGAAACAGTGATGTATCCCTACTACTCTAAGTGGA

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G62120.1 (Arabidopsis thaliana), 3'ss of exon 4
attgtttaagaactcatggtgctcatttgacaaaaatgttatgaattattttattaatcctatctcacctaatattttggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
|| || | | || || | | | | || | ||| | ||| | | | ||| |||| ||||| || ||||| ||||| || || |||| || |||||||| || ||||||||||||||||| |||||||| || ||||| || || || |||||||
------------------gtttgtatatcttgtagatcttgtttgtgaagaaa--aaggccttctta--taaca----gatctcattg--ttttgtttagGTTGCGTGGGTTACAAAGTCAGGTAAATCTGACTTGGAAGTCCCAATTGCTATTCGTCCAACCAGTGAGACAGTGATGTACCCTTACTACAGCAAGTGGA

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|352787275|gb|FQ477895.1|FQ477895
EST:     CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCCATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
EST: gi|161715595|gb|FC068351.1|FC068351
EST:     CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
EST: gi|30306282|gb|CB983076.1|CB983076
EST:     CTGGGGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
EST: gi|110712760|gb|EE088090.1|EE088090
EST:     CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
EST: gi|29784140|gb|CB344515.2|CB344515
EST:     CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
EST: gi|161708997|gb|FC058789.1|FC058789
EST:     CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
EST: gi|37190730|gb|CF610079.1|CF610079
EST:     CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
EST: gi|110713336|gb|EE089170.1|EE089170
EST:     CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
EST: gi|110712013|gb|EE089150.1|EE089150
EST:     CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAG                         GTCGCTCGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT
genomic: CTGGTGTTTTACAAAAGGAGAAGGATCACATTGAGGGTTTCGCTCCAGAGgtaagatttt ... tttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttattaatcctatctcacctaatattttggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
                                            ctttttcct  CT-rich tract
 taatattttggtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtttaagaactcatggtgctcatttgacaaaaatgttatgaattattttattaatcctatctcacctaatattttggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - -gaactca
- - - - - - - - tggtgct
- - - - - - - - - - - - - - -acaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgac