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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagttctgactaggttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT

Basic information

species Vitis vinifera
transcript Vv06s0004g05560.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagtt---ctgactag-gttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT
           || || |  ||  |    | ||  |   |  |     | | | |  ||     || ||  ||    |  | |     |     ||     ||||  ||||  | || | |    | || || || |  ||||| ||||| |||||| |||| || ||||||||||||||||| ||||||||||| || || | 
----------gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA

upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G059282_T01 (Zea mays), 3'ss of exon 1
tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagttctgactaggttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT
            | |  || |  ||     |||| || | | ||    |  ||       |           ||   || |  ||         |  ||||  ||||  | || | |   || || || |||   ||||| |||||   ||||| ||| || ||||||||||||||||||||||| ||||| || || | 
-----------gtagggtactcttcacctcttccattcccatcagcgcgccgtcctcgcatcacatcca---tccctctcgtcttcc-------ccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTA

upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G03990.1 (Glycine max), 3'ss of exon 1
tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagttctgactaggttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT
    |   ||  | ||  ||||   || ||  ||||| ||    ||     |||   | |||   |   | |  | |  |   |  ||  |  | |  |||||| || || || ||| | || || ||||| || || || ||||| |||||||||||||| |||||||| |||||||| || || |||  ||| |||||
---gttcgatactagt--attttattttatccccttttcactgtaattagggttccaagtttcaaaacta-taataataataataatttctttgat--agGGAGTTTCGCTGAGAGGCAGCACGGCGAAGTTACCTTTCCTGAGATCAGCACCACCATTCTCGAGAAGATTTGCCAGTACTTTTATTGGCATCTCCAATT

upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G41410.1 (Glycine max), 3'ss of exon 1
----tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagttctgactaggttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT
      ||| | |||||  | ||||  | |||    | |||     |||   |  |||   | |||   | | |  |   | ||  || |||| |       |||||| || || || ||| | || || ||||| || || || ||||| |||||||||||||| |||||||| |||||||| || || |||  ||| |||||
gttcgttattatattttattatatt-atattacccccttttctctgcaattagg-gttccaagtttcaaaatta--taataataatttctttgat-------agGGAGTTTCGCTGAGAGGCAGCACGGCGAAGTTACCTTTCCTGAGATCAGCACCACCATTCTCGAGAAGATTTGCCAGTACTTTTATTGGCATCTCCAATT

upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G59140.1 (Arabidopsis thaliana), 3'ss of exon 1
------tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagttctgactaggttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT
      |  || ||        |      || |||  || ||  |||    |   || | | ||   |   | | |||  |      ||| ||||||  | |  |||  | ||  |||||  | || |||| | ||| |||||||| || ||||||||||| || || |||||||| |||||||| ||||||||||||||||||| 
gtaatttgaataaagaagcaagtccaaattcataagatcattctcaatttca---ttatgtagatgctaa-atttagtaattctgttgttatttggtatggt--agGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATA

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:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|34319622|gb|CF372376.1|CF372376
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|30326539|gb|CD009801.1|CD009801
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|77582862|gb|DV220412.1|DV220412
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|30134710|gb|CB920048.1|CB920048
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|110401168|gb|EC967768.1|EC967768
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|110421660|gb|EC987960.1|EC987960
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|30330192|gb|CD013454.1|CD013454
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|110418444|gb|EC984601.1|EC984601
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|32271968|gb|CD721127.1|CD721127
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|110408935|gb|EC974583.1|EC974583
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|77578008|gb|DV217766.1|DV217766
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|110392803|gb|EC957238.1|EC957238
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|110371311|gb|EC935227.1|EC935227
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|71861463|gb|DT010518.1|DT010518
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|110701302|gb|EE078715.1|EE078715
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
EST: gi|22010533|gb|BQ795567.1|BQ795567
EST:     GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCG                         GGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA
genomic: GAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttcc ... tcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggttgtttggaatttgggagtgagttctgactaggttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT
                          ttctgac  putative branch site (score: 2)
                                     tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagttctgactaggttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT

- - - - - - - - - - - - - - - - - - - caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - tgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgac