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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccatgtagcccttgttgctattcgtttttgtatcacacttgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC

Basic information

species Vitis vinifera
transcript Vv19s0015g01730.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 14
gtaagcccatgtagcccttgttgctattcgtttttgtatcacact-tgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC-
        | ||  |  ||||     ||| | | | | ||   || |     | ||  ||   | || | | |    ||||    |     |  |    ||    | |||| ||||| |   |        | |  | |||  ||||||||| | || ||||||||||| |||||||| || || || |||||||| |||||||||||||||||  ||||| |||||||||||||||||||||||| 
-------taagtgactattgtcttggttcctctatatttcttgctctttttcctttgcaatgtgattaattctctcttgcttctttctttttattatgttgt--ttatgattttcatttgatt--------tttgcaccttttcaggCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTAACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATACC

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 14
gtaagcccatgtagcccttgttgctattcgtttttgtatcacacttgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC
|||||    |   | | | ||| || |   | | | |   |   ||    | | | | |  | ||     | | ||| || || ||    ||   |  |  |    || | ||||| |    |        ||    |||  ||||||||| | || ||||||||||| |||||||| || || || |||||||| || ||||| ||||||||  ||||| ||||||||||||||||||||||||
gtaagtgactaatgtcttagttcctctgtatctct-tgctaattttctttttactgtgattaattc--tctcttgcttctttctttttattgtgtcgtttaaa---tggttttcatttgatcg--------ctgctccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 11
gtaagcccatgtagcccttgttgctattcgtttttgtatcacacttgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC
|||||    |   |||  ||||| | ||| | | | ||||| |  |     ||||        | | | |||  | |||| || |||   |  |  ||   |    |||| | ||||||  | ||  || ||   || || |||||||||||| || || ||||||||||| ||||| || || || ||||| ||  | ||||||||||||||  ||||| ||||||||||||||||||||||||
gtaagttacttgtgcc--tgttgttgttcctctgtatatcatatatcttgccatttctt----tgttattttctgttgct-tctttcttttcttgtacctaa----tgatttgcatatatatatatgctctc---atattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCAAGAATAAAAATCCTGACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 14
gtaagcccatgtagcccttgt-tgctattcgtttttgtatcacacttgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC
        | ||  |   ||| || | ||| | | | ||||| |  |   ||    ||      | | | |||  | ||||   |||    | || | ||   | ||||     ||||||  || |  || ||   || || |||||||||||| || || ||||||||||| ||||| || ||||| ||||| || || ||||||||||||||  ||||| |||||||||  |||||||||||||
------gtaagttacttgtgtctgttgttcctctgtatatcatatat---cttgccattttttttgtcattttctgttgcttgtcttttt-tagtac-ctaatgttttg-----catata--tgcatgctctc---atattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCGAGAATAAAAATCGTGACATCTGAGATTGAGATTGGTTTGAATGAAGCATTCCGTGTCATAC

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT4G26510.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaagcccatgtagcccttgttgctattcgtttttgtatcacacttgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC
          |||  |  |    |    | |||  ||||||    |  || | || | |     ||     ||  |     |  | | || |    | || ||||     ||| | |||  |    | | |||   |   | ||||||||||| || || ||||||||||||||||  ||||| || |||||||| || |||||||| || |||  |||  | || ||||| || ||||| || |
----------gtaagc--taacacacaccctttgcgtatcatttatacaccccttgtga-----ttactccttatccatgtttatccacaag----aatgcagct---ggattgagatattt----tttttctttgttcaatcagGCACCTCAAGGTGTTCATGTGGTCTGCAAAAAATTCCCAAGAATAAAGATAGTGACATCTGAAATCGATAATGGGTTAAACGAAGAGTTTCGTGTTATTC

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|349818455|gb|FQ401069.1|FQ401069
EST:     TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCT                         GCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
genomic: TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCTgtaagcccat ... atcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
EST: gi|349825804|gb|FQ423099.1|FQ423099
EST:     TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCT                         GCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
genomic: TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCTgtaagcccat ... atcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
EST: gi|349832612|gb|FQ421970.1|FQ421970
EST:     TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCT                         GCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
genomic: TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCTgtaagcccat ... atcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
EST: gi|349808312|gb|FQ405456.1|FQ405456
EST:     TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCT                         GCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
genomic: TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCTgtaagcccat ... atcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
EST: gi|349824583|gb|FQ413250.1|FQ413250
EST:     TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCT                         GCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
genomic: TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCTgtaagcccat ... atcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
EST: gi|349809963|gb|FQ398588.1|FQ398588
EST:     TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCCGAATCTCATATCT                         GCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
genomic: TACAGAAGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCTgtaagcccat ... atcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
EST: gi|34362426|gb|CF404011.1|CF404011
EST:     AGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCT                         GCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT
genomic: AGGGTGTACCAGAGTCCAACATCATATTTCTGAATCTCATATCTgtaagcccat ... atcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC
                                       gtctaaa  putative branch site (score: 3)
                                              tcttacc  CT-rich tract
              tttgatattcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcccatgtagcccttgttgctattcgtttttgtatcacacttgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA