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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCAAGAAGAAAATTCCAGTTCTCATCCTCTGCAACAAAACTGACAAAGTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttcaacttaccctatttctgggttttggccttttgaataactgtcatctcattgattatcccggcaaataatttgatggaatgggtaacgcca...

Basic information

species Vitis vinifera
transcript Vv01s0127g00270.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00270.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os06g27870.1 (Oryza sativa), 5'ss of exon 4
TTGTCAAGAAGAAAATTCCAGTTCTCATCCTCTGCAACAAAACTGACAAAGTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggctt-caacttaccctatttctgggttttggccttttgaataact-gtcatctcattgattatcc-cggcaaataatttgatggaatgggtaacgcca
| || |||||||  ||||  ||||| ||  ||||||||||||| || ||||| || |||||  | || |||||||||| ||| ||| ||||||| ||||||||||| || |   ||  | |||          |  |   |  |  |||| || || ||||  || |||     | || | |||| ||   |  |  |     
TAGTGAAGAAGAGGATTCATGTTCTGATATTCTGCAACAAAACAGATAAAGTTACGGCTCACTCAAAAGAATTCATCAAGAAGCAATTGGAAAAAGAAATgtatggttttctttttgacgtatcatactagcataactagtgcatcaacttgtgatgtcatctataatcaatcactaagattttggtgtgttttgctata---

upper sequence: Vv01s0127g00270.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G03540.1 (Glycine max), 5'ss of exon 5
TTGTCAAGAAGAAAATTCCAGTTCTCATCCTCTGCAACAAAACTGACAAAGTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttcaacttaccctatttctgggttttggccttttgaataactgtcatctcattgattatcccggcaaataatttgatggaatgggtaacgc-ca
|||| | |||||| |||||||| || || |||||||||||||| |||||||| ||||||||||| || || || ||| | |||||  |||| ||||||||||||| |||||| |  ||  || | |    | |   |  || |        || ||  || || ||  |     ||  |    | | |||||  |    ||
TTGTGAGGAAGAAGATTCCAGTGCTTATTCTCTGCAACAAAACAGACAAAGTCACTGCTCATACTAAAGAGTTTATCCGAAAACAGATGGAGAAGGAAATgtatgccttcaagtc-ccaaatcttttatctctactcactttatccgtcagcaactgctttatgatttcattttattgtccagttggatgggacatatgca

upper sequence: Vv01s0127g00270.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G04110.1 (Glycine max), 5'ss of exon 5
TTGTCAAGAAGAAAATTCCAGTTCTCATCCTCTGCAACAAAACTGACAAAGTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttcaacttaccctatttctgggttttggccttttgaataactgtcatctcattgattatcccggcaaataatttgatgg--aatgggtaacgcca
|||| | |||||| |||||| | || || |||||||||||||| |||||||| ||||||||||| || || || ||| | |||||  |||| ||||||||||||| |||||| |  ||  || | |    | |   |  || |  ||    || ||  || || ||  |     ||  |    | |  ||| | |||     
TTGTGAGGAAGAAGATTCCAATGCTTATTCTCTGCAACAAAACAGACAAAGTCACTGCTCATACTAAAGAGTTTATCCGAAAACAGATGGAGAAGGAAATgtatgtcttcaagtc-ccagatcttttatctctactcactttatcaatcagcaactgttttatgatttcattttattgtcctgttgataattgataatagt-

upper sequence: Vv01s0127g00270.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G39250.1 (Glycine max), 5'ss of exon 5
TTGTCAAGAAGAAAATTCCAGTTCTCATCCTCTGCAACAAAACTGACAAAGTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttcaacttaccctatttctgggttttggccttttgaataactgtcatctcattgattatcccggcaaataatttgatggaat-gggtaacgcca-
| || | |||||| |||||  | || || |||||||||||||| |||||||| ||||||||| ||||||| |||||| | |||||  |||  |||||||||||| ||||  |   || | || | |    | ||    ||||| |     |    |  ||  || |  |     ||  || | ||   | || | |    | 
TCGTGAGGAAGAAGATTCCGTTACTTATTCTCTGCAACAAAACGGACAAAGTCACTGCTCATTCCAAGGAGTTCATCGGCAAACAGATGGGGAAGGAAATgtattgctttgag--actcaatcttttatctctgcttgtttgattgttcattgatttctttgttgttgcatagtattgttgggtgttgttggattatctgag

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|110379904|gb|EC945128.1|EC945128
EST:     GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAAT                         TGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
genomic: GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttc ... tgttttacagTGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
EST: gi|110713701|gb|EE089850.1|EE089850
EST:     GTAACTGCTCATACCCAGGAATTCATCAGGAAACAACTGGAAAAGGAAAT                         TGAGAAGTTCCGCGCATCAAGAAATGTAATATCAGCAGCTGATGTTGTG
genomic: GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttc ... tgttttacagTGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTG
EST: gi|37188251|gb|CF607600.1|CF607600
EST:     GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAAT                         TGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
genomic: GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttc ... tgttttacagTGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
EST: gi|34542592|gb|CF510824.1|CF510824
EST:     TAACTGCTCATAC-AGAGGAATTCATCAGGAAACAACTGGAAAAGGAAAT                         TGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
genomic: TAACTGCTCATACCA-AGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttc ... tgttttacagTGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
EST: gi|30329427|gb|CD012689.1|CD012689
EST:     GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAAT                         TGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
genomic: GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttc ... tgttttacagTGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
EST: gi|51051498|gb|CO819087.1|CO819087
EST:     GT-ACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAAT                         TGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
genomic: GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttc ... tgttttacagTGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
EST: gi|110372621|gb|EC936805.1|EC936805
EST:     GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAAT                         TGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
genomic: GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttc ... tgttttacagTGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
EST: gi|156729691|gb|EV233812.1|EV233812
EST:     GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAAT                         TGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA
genomic: GTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttc ... tgttttacagTGAGAAGTTCCGCGCATCAAGAAGTGCAATATCAGCAGCTGATGTTGTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCAAGAAGAAAATTCCAGTTCTCATCCTCTGCAACAAAACTGACAAAGTAACTGCTCATACCAAGGAATTCATCAGGAAACAACTGGAAAAGGAAATgtatggcttcaacttaccctatttctgggttttggccttttgaataactgtcatctcattgattatcccggcaaataatttgatggaatgggtaacgcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtaac