Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaattaaatttgtgagacaatatgtacctttgtgttggattggaatggctcaacattgtctcagcttactaaaatagtgctcaatgtgcctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCATGGTCAGTTTGCATTTACAACTAGTGAGGCTGGCAACTACCTCGCCTGTT

Basic information

species Vitis vinifera
transcript Vv12s0034g01440.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0034g01440.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G30330.1 (Glycine max), 3'ss of exon 1
-----tttaattaaatttgtgagacaatatgtacctttgtgttggattggaatggctcaaca-ttgtctca-gcttactaaaatagtgctcaatgtgcctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCATGGTCAGTTTGCATTTACAACTAGTGAGGCTGGCAACTACCTCGCCTGTT
     | |  ||   | | |||   |  |  | |   |        ||  || ||   |  | |||||||  | || ||||  ||||    ||| ||  || | ||||| |||||||||||||| |||||||| ||||||||||||||    || |||||| |  |||||||||| |||   |||||||| |||||||| || || |
gtaattctggttggctct-tgaatgacaaccttctgatacagcttgttataaaggtctattacttgtctcttggtttctaa--tagt----aatttgtttcctttagGTGACATCACCATATGGAAACAATCTTCATCACAAGGAGAACACAACACATGGTAATATTGCATTTACGACTCAAGAGGCTGGGAACTACCTTGCATGCT

upper sequence: Vv12s0034g01440.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G13470.1 (Glycine max), 3'ss of exon 1
-----tttaattaaat-ttgtgagacaatatgtacctttgtgttggattggaatggctcaaca-ttgtctca-gcttactaaaatagtgctcaatgtgcctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCATGGTCAGTTTGCATTTACAACTAGTGAGGCTGGCAACTACCTCGCCTGTT
     | |  ||   | |||   |||||  |     | |  | ||  ||  |  ||   |  | |||||||  | || ||||  ||||    ||| ||  |  | ||||| |||||||| ||||| |||||||| ||||||||||||||    || ||||||    ||||||||||||||   |||||||| |||||||| || || |
gtaattctggttggctcttgaatgacaaccttctgatatcagctg--ttatagaggtctattacttgtctcttggtttctaa--tagt----aatttgtttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACATGGTAGTATTGCATTTACAACTCAAGAGGCTGGGAACTACCTTGCATGCT
















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|349808549|gb|FQ405693.1|FQ405693
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|351026894|gb|FQ436547.1|FQ436547
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTGACATCACCATATGGGAACAATTTACATCACAAGGATAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|161712149|gb|FC061521.1|FC061521
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|77587717|gb|DV223037.1|DV223037
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|351016734|gb|FQ424161.1|FQ424161
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGTCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|77581489|gb|DV219683.1|DV219683
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|349826899|gb|FQ418990.1|FQ418990
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGATAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|351028478|gb|FQ444759.1|FQ444759
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGATAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|110390944|gb|EC955893.1|EC955893
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|351031396|gb|FQ445421.1|FQ445421
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|351034240|gb|FQ448037.1|FQ448037
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|161710012|gb|FC059773.1|FC059773
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|294966274|gb|GW837525.1|GW837525
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|351014680|gb|FQ437880.1|FQ437880
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|71877423|gb|DT026478.1|DT026478
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|351029626|gb|FQ427466.1|FQ427466
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
EST: gi|351017782|gb|FQ436135.1|FQ436135
EST:     TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAG                         GTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT
genomic: TCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgtttgttttt ... cctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggctcaacattgtctcagcttactaaaatagtgctcaatgtgcctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCATGGTCAGTTTGCATTTACAACTAGTGAGGCTGGCAACTACCTCGCCTGTT
                       tactaaa  putative branch site (score: 1)
                                           tgcctctt  putative PPT
                      ttactaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaattaaatttgtgagacaatatgtacctttgtgttggattggaatggctcaacattgtctcagcttactaaaatagtgctcaatgtgcctcttatagGTAACATCACCATATGGGAACAATCTACATCACAAGGAGAATGTGACTCATGGTCAGTTTGCATTTACAACTAGTGAGGCTGGCAACTACCTCGCCTGTT

- -aattaaa
- - - - - - - -gagacaa
- - - - - - - - - - - tatgtac
- - - - - - - - - - - - - - - - -gtgttgg
- - - - - - - - - - - - - - - - - - - - - - - - -gctcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaatg