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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgacaaattattatcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG

Basic information

species Vitis vinifera
transcript Vv12s0059g01930.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
-------------------------------------ccttgacaaattatt---atcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgg-gatcattt-------acacttcctata--------ttgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG
                                     |  ||   |  |||     |   ||||||||    |       ||   ||     |   |   | || ||   ||   |||| | |         | ||  | ||        |||||||| |||||| || |||||||||||||||||||| | |||||| ||||||| ||||||||| | |||
gtaagtgtgcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 10
----ccttgacaaattattatcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG
    |  ||  |  |  | ||   | ||      | |   ||  ||    | |         |||   ||   ||    ||  || |||||| || |    |||||||| ||| | |||||||||||| ||||||||||||||||||| |||||  |    ||  | |||
gggactctgggagttcgtgat---gctttgcttaatttatttgattggcatgtctcatacaattgattgagtcatcaacattgttcacactttcttt-cgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 9
ccttgacaaattattatcagg--attcatgg--tagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG
  ||||   | ||| ||  ||  |||| ||    ||||  ||    | |||| |  |   |  |     |   |         |  ||| ||  | | |  |||||||| ||| | |||||||||||| ||||||||||||||||||||||||| |||   ||  |||||
--ttgatcgaatat-attgggttattcttgaataagtgaattcacatatttcctggtaactgctcactcatttacactatctttccacatttt-tgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 11
--------------------------------------------------------------------------------------------------ccttgacaaattattatcaggattcatggtagtggcttt--ttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG
                                                                                                   |||   ||||| | || |  | ||||  ||||  | ||  |        |  |||| |  |       | |      | ||  ||||  | | |  |||||||||||||| || ||||||||||| ||||||| || |||||| |||| || ||||||||  | |||
gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatc-tagtatccttgatgcgaaacataattctatggttcttttggtaacctagtaatccacacg-cttgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 10
----ccttgacaaattattatcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG
     ||| || |||       |      ||  |  ||  ||  ||    |    |  ||  ||   |      ||   |   ||| |  ||  | | |  |||||||| ||| |  |||||||||| |||||||||||||||||||| || || ||| | ||  |||||
tcactctttaccaatcgacgctacatccaataatcatgtattggttggcatagcttatttagttcctaagtaattt---actgttt-ctttttatgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGCATCGGTGTCATTCAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 9
---------------------------ccttgac----aaattattatcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG
                             ||| |    || |||||||     |||      | ||  || | | | |     ||    |   | |    | |   | || | ||   ||||  ||| |||||| ||||| ||||||| ||||| || |||||| ||||||||||||| || || |||||| |||||
gtaagtaccaattgtgttactactattttttggcttctaatttattattctccttccaaagggaggggttatatatattcatgtcacgatgacatgtttaaatcataccaat-acttgtcctgaattacagATACTCTACTTTATTGGGTTTGGTTTTTTCTGCATTGAATCACTGCTGAGCATTTGGGTTATTCAG

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|110418607|gb|EC984768.1|EC984768
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|77584192|gb|DV221151.1|DV221151
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTC
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTC
EST: gi|110385536|gb|EC950069.1|EC950069
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|110394878|gb|EC960262.1|EC960262
EST:     GGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: GGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|110388736|gb|EC953515.1|EC953515
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|110376126|gb|EC941168.1|EC941168
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|32246966|gb|CD712785.1|CD712785
EST:     CTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: CTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|32245954|gb|CD711773.1|CD711773
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|71870414|gb|DT019469.1|DT019469
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|110423904|gb|EC990257.1|EC990257
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|71870410|gb|DT019465.1|DT019465
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|110422592|gb|EC988919.1|EC988919
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGT
EST: gi|37190516|gb|CF609865.1|CF609865
EST:     AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGG                         ATATTCTACCTTATTGGA
genomic: AGGAATCCTGCCTGCAGTGGATCTTTTGAGTAAACATGCTTTAGTTGGGgtaagttcca ... tatattgcagATATTCTACCTTATTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG
                                      cacttcct  CT-rich tract
         ttttttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgacaaattattatcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG

- - -acaaatt
- - - - - - - - - - - ttcatgg
- - - - - - - - - - - - - - - - tggcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttcc