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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttctaactatatacagtttcctaaaacacaataatattttgcttttcatttctttggttgggtgtaaattgataggattgtgcatgggatatgacaccacctattctgctgtgactttaatctaatgccagaaatagcattacaaagcctgaccgttttgtttttcttttttctttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTTGCCTCAGAAAGCTTTAATATCTGAAGAATAATCAGTTTCTTTTAAGTTG

Basic information

species Vitis vinifera
transcript Vv06s0004g05560.t01
intron # 3
splice site 3'
intron type U2

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|77578280|gb|DV217915.1|DV217915
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|34319622|gb|CF372376.1|CF372376
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|32457151|gb|CD798325.1|CD798325
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|30326539|gb|CD009801.1|CD009801
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|32456769|gb|CD797943.1|CD797943
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|77582862|gb|DV220412.1|DV220412
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|30134710|gb|CB920048.1|CB920048
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|110401168|gb|EC967768.1|EC967768
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|110421660|gb|EC987960.1|EC987960
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|30330192|gb|CD013454.1|CD013454
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|110413425|gb|EC979210.1|EC979210
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|22015221|gb|BQ800255.1|BQ800255
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGTTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|110418444|gb|EC984601.1|EC984601
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|30127262|gb|CB912601.1|CB912601
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|32271968|gb|CD721127.1|CD721127
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|110408935|gb|EC974583.1|EC974583
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|77578008|gb|DV217766.1|DV217766
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|110392803|gb|EC957238.1|EC957238
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|110371311|gb|EC935227.1|EC935227
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|71861463|gb|DT010518.1|DT010518
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCCTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|110701302|gb|EE078715.1|EE078715
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT
EST: gi|22010533|gb|BQ795567.1|BQ795567
EST:     GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTG                         GGGTCTTTACTGACTAACTGTTCATTGGAGATACAACAGGACAGCTGTGTT
genomic: GAGGGGATCACTGTTTTTGCTTCTGGGGCCACAAGTCCCTTTGAATGTTGgtaagccttc ... ttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatagcattacaaagcctgaccgttttgtttttcttttttctttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTTGCCTCAGAAAGCTTTAATATCTGAAGAATAATCAGTTTCTTTTAAGTTG
                 gcctgac  putative branch site (score: 3)
                  cctgaccgttttgttt  CT-rich tract
                          ttttgtttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccttctaactatatacagtttcctaaaacacaataatattttgcttttcatttctttggttgggtgtaaattgataggattgtgcatgggatatgacaccacctattctgctgtgactttaatctaatgccagaaatagcattacaaagcctgaccgttttgtttttcttttttctttttctgcagGGGTCTTTACTGACTAACTGTTCATTGGAGATACAATAGGACAGCTGTGTTGCCTCAGAAAGCTTTAATATCTGAAGAATAATCAGTTTCTTTTAAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA