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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgctttattttattgattagccattttttagcgtgttgggtcatggaactccgattgatttttcttatacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGATTAACATTGGGCATTTAGATGAGAGTGGAACTTACACCGGTCAATTTACT

Basic information

species Vitis vinifera
transcript Vv14s0060g02110.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G134109_T01 (Zea mays), 3'ss of exon 2
gtatgct-gctttattttattgattagccattt---tttagcgtgttgggtcatggaactccgattgatttttcttatacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGATTAACATTGGGCATTTAGATGAGAGTGGAACTTACACCGGTCAATTTACT
||| | | ||| || ||| ||| |||  | |||    |  || || |   | |||        ||      ||  | | |||||||||| ||||| |||||| |||||||| | ||||||||||| || |||||||| |||||||| || || |||| || |||    |||   ||||| || || 
gtacgtttgctgtactttcttgtttaaacctttgccctctgcatggttaattatgttgtgttaatattgagtttctgttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTACGATGGTCACTTCACC

upper sequence: Vv14s0060g02110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G37700.1 (Glycine max), 3'ss of exon 1
gtatgctgctttattttattgattagccattttttagcgtgttgggtcatggaactccgattgatttttcttatac-ttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGATTAACATTGGGCATTTAGATGAGAGTGGAACTTACACCGGTCAATTTACT
    | ||     |||| | || | |   || ||| | |   |  |   ||    |   |||| |    |   ||| ||||| |||||||||||| || ||||| ||| ||||||| ||||| || || ||||| |||||||| ||||| ||||||| ||| |  || |              
----gttgtcacgttttttcgaattgtggttcttttgtggaatttgaactgatgtt---attgttaaagCACGTACGTTGCAACTCTGCCACTAACAGACTCATAACTGCAAAGGACCATGCCTCGGTTCAGATAAACATTGGCCATTTGGATGAGAATGGTATCTATA--------------

upper sequence: Vv14s0060g02110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G53890.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------gtatgctgctttattttattgattagccatt--ttttagcgtgttgggtcatggaactccgattgatttttctt----atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGATTAACATTGGGCATTTAGATGAGAGTGGAACTTACACCGGTCAATTTACT
                          || |   | || |||  | |  | ||| | |  | |||      | |   | |    | | |||| | | |  |    ||   |  ||||| || || || ||  | ||||| |||||||||||||| ||||| ||| |||||||||| ||| | ||||  | |||    ||||| || ||||| || 
gtatatatcagctctctttgttctctgtgtaacgtttgattaaaatcttaagctaattgtcttaattaagtagcctaagctgattctattgttgtgtaatggtaatttgtttagCTCGGCAACAAACAGAATGATCACATCAAAGGATCATGCTTCAGTTCAGCTTAACATTGGTCATCTTGATGCTAATGGTCTCTACACTGGCCAATTCACC

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|77584391|gb|DV221265.1|DV221265
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|34320516|gb|CF373270.1|CF373270
EST:     ATGCAGAACGAAGAGGGACAAACCATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|77587917|gb|DV223161.1|DV223161
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|110372534|gb|EC936710.1|EC936710
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|110691741|gb|EE070187.1|EE070187
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|110385849|gb|EC950405.1|EC950405
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|71879577|gb|DT028632.1|DT028632
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|34416942|gb|CF415696.1|CF415696
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|110696100|gb|EE074877.1|EE074877
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|110396771|gb|EC962470.1|EC962470
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|110425492|gb|EC991877.1|EC991877
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|34415798|gb|CF414552.1|CF414552
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|110695764|gb|EE074157.1|EE074157
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
EST: gi|110412806|gb|EC978567.1|EC978567
EST:     ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTG                         CTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT
genomic: ATGCAGAACGAAGAGGGACAAAACATGGATCTTTACATCCCTAGGAAGTGgtatgctgct ... atacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttttagcgtgttgggtcatggaactccgattgatttttcttatacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGATTAACATTGGGCATTTAGATGAGAGTGGAACTTACACCGGTCAATTTACT
                               gattgat  putative branch site (score: 4)
                                     tttttcttatactt  CT-rich tract
                                attgatttttcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgctttattttattgattagccattttttagcgtgttgggtcatggaactccgattgatttttcttatacttgcagCTCTGCCACTAATAGGCTCATCACTTCAAAGGATCATGCATCAGTCCAGATTAACATTGGGCATTTAGATGAGAGTGGAACTTACACCGGTCAATTTACT

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