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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttgcaatttggggaagaaaagctgttgataaaggatttgattctgagcatactgattatctcttgaaataatacatttgtttgatttgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCTGCGGAGTACAGCGGTATCAAAGTTGAACTGGTTCAGAACTTTGAGATGG

Basic information

species Vitis vinifera
transcript Vv12s0035g01130.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G00470.2 (Glycine max), 3'ss of exon 1
atttttgcaatttggggaagaaaagctgttgataaaggatttgattctgagcatactgattatctc--ttgaaataatacatttgtttgatttgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCTGCGGAGTACAGCGGTATCAAAGTTGAACTGGTTCAGAACTTTGAGATGG
                           ||   |  | |  ||  |        ||| | ||| |    ||  | | |  || |  | | | |   |||  || || ||||||| |||||||| ||||||||| ||||||||||||||||||| || |||||    ||  || |||||||  | |  |  || ||||||||||
---------------------------gtgagtctaagcctttctctcagatttac-gcttaacagagttacagtcactcagtaatct-actccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCAGCCGAGTATGCTGGCGTCCAAGTTGATTTTGCCCCTAATTTTGAGATGG

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G40330.1 (Glycine max), 3'ss of exon 2
atttttgcaatttggggaagaaaagctgttgataaaggatttgattctgagcatactgattatctcttgaaataatacatttgtttgatttgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCTGCGGAGTACAGCGGTATCAAAGTTGAACTGGTTCAGAACTTTGAGATGG
                                    |  |     | |   | ||    |||   |||  | | |  || |    | | |   |||  || || ||||||  || ||||| ||||||||| ||||||||||||||||||| ||||||||   |||  || |||||||  | |  |  || ||||||||||
----------------------------------gtgagtccagatttacacttaagagtta---cttacactcactcactaacct-actccttttctagATCCTGCATGGTGGAAAAACCAACAAAAATTCTTACAAGACACTCATTGCGGCGGAGTATGCCGGCGTCCAAGTTGACTTTGCCCCAAATTTTGAGATGG
















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|351055139|gb|FQ440478.1|FQ440478
EST:     ATCTAAATCGAAGGGAGGCGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|161712238|gb|FC061612.1|FC061612
EST:     AAAGATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: AAAGATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|110368464|gb|EC932441.1|EC932441
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|161719271|gb|FC068941.1|FC068941
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|110727170|gb|EE103626.1|EE103626
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|110385087|gb|EC949579.1|EC949579
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|351042107|gb|FQ456317.1|FQ456317
EST:     ATCTAAATCGAAGGGAGACGTTTTTCTGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|351017433|gb|FQ435786.1|FQ435786
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|110381916|gb|EC937999.1|EC937999
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|37183980|gb|CF603334.1|CF603334
EST:     GGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: GGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|37183445|gb|CF602799.1|CF602799
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|351028342|gb|FQ427238.1|FQ427238
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|110374475|gb|EC939254.1|EC939254
EST:     TC-AAGATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: TCAAAGATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|110381825|gb|EC935490.1|EC935490
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|110392524|gb|EC958004.1|EC958004
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|351025275|gb|FQ434288.1|FQ434288
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|71855580|gb|DT004635.1|DT004635
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCGTGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|71859460|gb|DT008515.1|DT008515
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|71858356|gb|DT007411.1|DT007411
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|294965707|gb|GW839162.1|GW839162
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|351027331|gb|FQ444580.1|FQ444580
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAGGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|161714380|gb|FC063221.1|FC063221
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|351016802|gb|FQ424229.1|FQ424229
EST:     ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
EST: gi|352794288|gb|FQ479530.1|FQ479530
EST:     ATCTAAATCGAAGGGAGACGTTTTTCTGATAAGCCATGGCTCTG                         GTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT
genomic: ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTGgtgagttgat ... tgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgagcatactgattatctcttgaaataatacatttgtttgatttgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCTGCGGAGTACAGCGGTATCAAAGTTGAACTGGTTCAGAACTTTGAGATGG
                                           tttgcttt  CT-rich tract
                        aaataatacatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttgcaatttggggaagaaaagctgttgataaaggatttgattctgagcatactgattatctcttgaaataatacatttgtttgatttgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCTGCGGAGTACAGCGGTATCAAAGTTGAACTGGTTCAGAACTTTGAGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- ttttgca
- - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - gataaag
- - - - - - - - - - - - - - - - - - - - - - - - - gcatact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaataa