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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC

Basic information

species Vitis vinifera
transcript Vv03s0038g04500.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 7
gttcgtggattttattctttgaaagtttatgtggtggactc-tatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                    | |||||| | |   |  |    ||   | ||||   |  | ||| | |   |      || | |    | |    ||  | |  |  ||      |||| ||||  |||||||||||||||||||||||  |||| ||||||||| |  | ||||| ||| |||||||||||||||||||  | ||| | || ||||||
--------------------gtaagtttttctctcgcccctacatacctatcgatgtaccaatctatctgtccatctaggtctctaaggactaaggactaactatttgta------acagATATACCGACATGCATGCTGACTATACTGGTAAAGGCTTTGATCAGCTAATGGATGTGATTGACAAGATCAAGAATAATCCTGACGATAGGCGAATTATC

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 3'ss of exon 5
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttct--ccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                |||||||| |||          |||| | | ||||            | ||| ||  |  |  | | |||  | || ||  |  |   | | | |||||||  || |||| ||||||||||||||||||    ||  |||| |||||||||||  | ||||| ||| |||||||||||||||||||  ||||| || | || || 
---------------actttgaaactttcctct-----ctctctctctctctctctctctccatatttccttaactttatctatctgactagattctaatttccg-tgaaatattttgtagATATACTGACATGCATGCTGACTACGTGGGAAAAGGTTTTGATCAGTTAATGGATGTCATTGACAAGATCAAGAATAATCCCGATGATAGAAGAATCATT

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 6
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                                 ||   ||    ||   |    | ||   | | |||| ||         ||  ||  |||||    ||  | | | |||| | |||| |||| ||||||||||||||||||||||||  |||| ||||||||| |  | ||||| ||| ||||||| ||||| |||||  |||| || || || || 
---------------------------------gtaagcttacattcctttccttgagctgtatcttttttc---------ttgttcatgttttctgataaagttgacatatctgacagATATACTGACATGCATGCTGACTATACTGGAAAAGGCTTTGATCAGCTAATGGATGTGATTGACAAGATTAAGAACAATCCTGATGACCGCCGAATAATT

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 7
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                                 ||   ||  |||  ||||   |     |  |||| ||||       || |||     ||||    ||  |   | |||||| |||| || | ||||||||||||||||||||| ||  |||| ||||||||| |  | ||||| ||| |||||||||||||| ||||  | || || || || || 
---------------------------------gtaagctacattcctctcctctcttc-tcgtgttgtctcttttcttttgttcatgtattttttgataaagtagacatatttgacagATACACTGACATGCATGCTGACTATACGGGAAAAGGTTTTGATCAGCTAATGGATGTGATTGACAAGATCAAGAATGATCCTGACGACCGTCGAATAATT

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 7
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                    | ||||  |||||     || ||| ||| |  ||| |  |  |||  ||      ||||  || |||   | |  |  | |      || ||||||||| |||| ||||||||||||||||||  |||||||||||||||||||| | |||||||||||||||||||| ||| ||||||| ||||||||| |||| || 
--------------------gtaagtggatgtgc----ctttatctttgt-aagtcattaggctgcatttc----gtaggattgctcagctctgtatttctcatc--tacattttacagGTATACTGACATGCATGCTGACTACTCTGGCCAAGGATTTGATCAGCTTTTAGATGTTATTAACAAGATAAAGCATAATCCCAATGATCGAAGGATCATT

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 6
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctca--tatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                    | ||||  |||||     || ||| ||| |  ||| |  |  |||  || |    ||||  || ||  |||| |    |||| ||||  || ||||||||| |||| ||||||||||||||||||  | |||||||||||||||||| | |||||||||||||||||||| ||| | |||||  |||||||| |||| || 
--------------------gtaagtggatgtgc----ctttatctttgt-aagtcattaggctgcatttt----gtaggattgctt-agttctg---tatttctcatctacattttacagGTATACTGACATGCATGCTGACTACTCCGGCCAAGGATTTGATCAGCTTTTAGATGTTATTAACAAGATAAAGCACAATCCTGATGATCGAAGGATCATT

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 7
gttcgtggattttattctttgaaagtttatgtggtggactctatttttct-cgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                    |||| | ||  |  | |  | | |||| ||    |||        | ||  |    || |  || ||| | | || |     |||   || |||||| || |||| ||||||||||  ||||||  | || ||||| ||||||||| | |||||||||||||||||||| ||| |||||||  ||||||| || ||||| 
---------------gtagggaaactatacctttttgttttttttttcctgttggtattacaatagattgttttgtgtggaattgctcaactctttattcgatgcct-tacattttatagATATACTGACATGCATCATGACTACTCCGGTCAAGGGTTTGATCAGCTTTTAGATGTTATTAACAAGATAAAGCATAATCCTGATGATCGGCGAATTATT

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 7
gttcgtggattttattctttgaaagtttatgtggtggactctatttttct-cgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                        ||    |   |  ||  | ||||||| |  |||        | ||  |    |  |  || ||| | | || |     |||   || ||| || || |||| ||||||||||  ||||||  | |||||||| ||||||||  | |||||||||||||||||||| |||  ||||||  ||||||| || || || 
------------------------gtaggggaactataccttttttttctgctggtattacaatagattgttttgtgaggaattgctcaactctttattcgctgcct-tacattctatagATATACTGACATGCATCATGACTACTCCGGCCAAGGGTTTGATCAACTTTTAGATGTTATTAACAAGATAAAGCGTAATCCTGATGATCGGCGAATCATT

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatat-tttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                                 || |  ||| | ||        |    |||||  || | |    |    ||     ||    || | ||| |||| | | | ||||| || |  || ||||||||||| |||||||||||||||||||||||| | |||||||| ||||||||||||||||| |||||  |||||||||||||||| 
-----------------------------gtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 7
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
       |    ||   ||| || |  |||||  |||  | |  || |||      | |  | ||||||   ||   | | ||||||                      | |||||||| || |  || ||||||||||| |||||||| ||||||||||||||  |  ||||||| ||| |||| |||||||| |||||  ||||||| || ||||| 
-------gtcagtaacttttcaatgcatatgt--tggttttttcttctctgttccgatggatttgttttggtgaaaca-tctttctct---------------------tgttttacagGTACACAGATATGCATGCTGATTATACTGGTCAAGGATTTGATCAACTTGTAGATGTAATTGACAAAATCAAGAACAATCCTGATGATCGGCGTATTATA

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|33401638|gb|CF207265.1|CF207265
EST:     GGTGACTCGGGACCCATATATGGGTTCCAGTGGAGGCACTTTGGTGCTAG                         CTATATTGACATGCATGCTGACTATACTGGCCAAGGGTTTGATCAGTTGTT
genomic: GGTGACTTGGGACCCATATATGGGTTCCAGTGGAGGCACTTTGGTGCTAGgttcgtggat ... tattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTT
EST: gi|110361466|gb|EC924940.1|EC924940
EST:     GGTGACTTGGGACCCATATATGGGTTCCAGTGGAGGCACTTTGGTGCTAG                         CTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTT
genomic: GGTGACTTGGGACCCATATATGGGTTCCAGTGGAGGCACTTTGGTGCTAGgttcgtggat ... tattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTT
EST: gi|110413975|gb|EC979795.1|EC979795
EST:     GGTGACTTGGGACCCATATATGGGTTCCAGTGGAGGCACTTTGGTGCTAG                         CTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTT
genomic: GGTGACTTGGGACCCATATATGGGTTCCAGTGGAGGCACTTTGGTGCTAGgttcgtggat ... tattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC
                          ttttaac  putative branch site (score: 2)
                                        tcatatattttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatattttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA