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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactccatcatttgattaattaataacaatacttatcaatccaacgccccatgttgatcaatattcttgactaccaaacacgtttgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGC

Basic information

species Vitis vinifera
transcript Vv01s0011g06290.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G09880.2 (Glycine max), 3'ss of exon 4
-gtaactccatcatttgattaattaataacaatactta--tcaatcca-acgccccatgttgatcaatattcttgactaccaaacacgtttgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGC
  | | |    | ||  ||  ||       ||   |||  || ||  | |    ||||||| || ||  |  || |  |    |||| |   |   | ||||||||||    || |||  | | || |  || ||||||||||||||||| || |||||||||||||||||||| ||    |||||  | || |  ||||
aatcatttgtacgttgtatatatatccgttaacttttacatctatatatatattccatgttaattaaattggttaatcattgtacacttaactaaaatagGATGTGGATTTAGCTTTACAACAATCAAATGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCGTGCACGGTAATACGGATGAGC

upper sequence: Vv01s0011g06290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G26920.1 (Glycine max), 3'ss of exon 6
--gtaactccatcatttgattaatt--aataacaatacttatcaatccaacgccc-catgttgatcaatattcttgactaccaaacacgtttgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGC
   |||    |    |  ||| ||   || || ||| | |||  ||  | |      | |||| | ||| |   | | |     |||| |   |     |||| |||||   ||| |||  | | || |  || ||||||||||||||||| || |||||||||||||||||||| ||    |||||  | || |  ||||
atataaaataaaatgtaaattcatgcaaagaaaaattcatatatatgaatcatttgtacgttgtttaat-tggctaattgttgtacacttaatttaattagGACGTGGATTTGGCTTTACAACAATCAAATGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCTTGCACGGTAATACGGATGAGC
















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|56688100|gb|CX126003.1|CX126003
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688146|gb|CX126049.1|CX126049
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688532|gb|CX126435.1|CX126435
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|30324780|gb|CD008042.1|CD008042
EST:     TGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: TGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|110361763|gb|EC925259.1|EC925259
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688821|gb|CX126724.1|CX126724
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688240|gb|CX126143.1|CX126143
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGTTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAATAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|161715966|gb|FC068755.1|FC068755
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCA
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCA
EST: gi|110405384|gb|EC970925.1|EC970925
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|30330531|gb|CD013793.1|CD013793
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|110378747|gb|EC943895.1|EC943895
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|30128027|gb|CB913366.1|CB913366
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|30127523|gb|CB912862.1|CB912862
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|34542274|gb|CF510506.1|CF510506
EST:     GCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGAGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: GCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|110427573|gb|EC994020.1|EC994020
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688741|gb|CX126644.1|CX126644
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|30125391|gb|CB910730.1|CB910730
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688020|gb|CX125923.1|CX125923
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|349811174|gb|FQ406162.1|FQ406162
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|71867743|gb|DT016798.1|DT016798
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|110701614|gb|EE079386.1|EE079386
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|161717827|gb|FC064740.1|FC064740
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGG
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGG
EST: gi|161719167|gb|FC065431.1|FC065431
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|30126050|gb|CB911389.1|CB911389
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688831|gb|CX126734.1|CX126734
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAACCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688837|gb|CX126740.1|CX126740
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688383|gb|CX126286.1|CX126286
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688239|gb|CX126142.1|CX126142
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|110385343|gb|EC949857.1|EC949857
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|27586836|gb|CB009531.1|CB009531
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
EST: gi|56688885|gb|CX126788.1|CX126788
EST:     ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAG                         GATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT
genomic: ACTGGAAGGGCGTCCTTCCCCGTCAGGCTTATCTCTCAAACCTCCTCCAGgtaactccat ... tgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaacgccccatgttgatcaatattcttgactaccaaacacgtttgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGC
                         tcttgac  putative branch site (score: 3)
                 atcaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactccatcatttgattaattaataacaatacttatcaatccaacgccccatgttgatcaatattcttgactaccaaacacgtttgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG