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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctttgcctctctctctctctctctctctcacccacacacacactcacagaaaaataactagtagctaactctgtgaattggtgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCTTTTAAAGGCTGCTG

Basic information

species Vitis vinifera
transcript Vv05s0124g00360.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
gtctctttgcctctctctctctctctctctctcacccacacacacactcacagaaaaa-------taactagtagctaactctgtgaattggtgggt------gatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCT-TTTAAAGGCTGCTG
   |||    |||| |   |           | |  ||||       | | ||  |         |  ||  |  |  ||  |    | |  ||         ||||||||| ||||| || |||||||| || || || |||||||||||||| || ||||| |||||||| || ||||||||| |    || ||  | | | |      
--gtctcgatctctatacatgcacacaatatttatacacatgagtcatgatagtcatcctttccttctcttttcccccacatttctcactactgcactttctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC-

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 7
---gtctctttgcctctctctctctctctctctctcacccacacacacactcacagaaaaataactagtagct---aactctgtgaattgg-tgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCT--TTTAAAGGCTGCTG
     |  ||| || |    |     ||||| |             ||| | |       ||   |  | | |   | | || |   ||||        ||||||| || || ||||||||| | ||||| || |||||||| |||||| |||| || |||||||| ||||||||||| ||    || ||  || ||      |  
gtcaacattttaccccctcgtacacgtctctgtgaatgatgtttttacattaatttggccatcttttattgatgtaatccctttcccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC--

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G001668_T01 (Zea mays), 3'ss of exon 7
gtctctttgcctctctctctctctctctctctcacccacacacacactcacagaaaaataactagtagctaactctgtgaattggtgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCT--TTTAAAGGCTGCTG
     |   | | |  | ||   |     ||||    |   |     | |||  ||  |  | |     ||    ||| |     |   |  ||||||| || || ||||||||  ||||||  ||||||||||| |||||| |||| || |||||||||||||| ||||| ||    || ||  || ||      |  
----gtcgacattttacccttcatactcgtctccgtgaatgatgtttttacattaatttggccatcttttattgatgtaatccctttcct--tgcagCTTGCTGCAGTGGCAGCTCTATGTGCACAGTACGAAGCAGAGTTCAGGCCCAACATGAGCATCGTTGTTAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC--

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 8
gtctctttgcctctctctctctc-tctctctctcacccacacacac--------------actcacagaaaaa-------------------taactagtagctaactctgtgaat-----tggtgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCTTTTAAAGGCTGCTG
|| | | |  |||| |||| ||| |||   |  |||   ||||                 ||||    | |||                    | ||  | | | ||  |   |||     | || ||  || ||||| |||||||| || ||  | || || ||||| |||||||||||  |||||||||||||||| ||||| || || |||||||| ||| | ||| || | |
gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaacaatgcttattgttggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCCG

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
gtctctttgcctctctctctctc-tctctctctcacccacacacac-----------actcacagaaaaataactagtagctaactct----------------gtgaattg--------gtgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCTTTTAAAGGCTGCTG
|| ||| |  || | |||| ||| |||      ||| ||||                |||||   | |||   || ||   |   |||                 | ||  |        || |    ||||||| | |||||| || ||| | || || ||||| |||||||||||  |||||||||||||||| ||||| || || |||||||| ||| | ||| || |||
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG

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|110361162|gb|EC924615.1|EC924615
EST:     GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAG                         CTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGGTGAGTTCCGGCCA
genomic: GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAGgtctctttgc ... ggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
EST: gi|110418740|gb|EC984911.1|EC984911
EST:     GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAG                         CTGGCCGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
genomic: GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAGgtctctttgc ... ggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
EST: gi|110363425|gb|EC927009.1|EC927009
EST:     GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAG                         CTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
genomic: GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAGgtctctttgc ... ggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
EST: gi|110400981|gb|EC967571.1|EC967571
EST:     GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAG                         CTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
genomic: GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAGgtctctttgc ... ggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
EST: gi|156738849|gb|EV242970.1|EV242970
EST:     GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAG                         CTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
genomic: GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAGgtctctttgc ... ggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
EST: gi|110380468|gb|EC945736.1|EC945736
EST:     GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAG                         CTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
genomic: GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAGgtctctttgc ... ggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
EST: gi|30302005|gb|CB978799.1|CB978799
EST:     GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAG                         CTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA
genomic: GTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAGgtctctttgc ... ggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacactcacagaaaaataactagtagctaactctgtgaattggtgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCTTTTAAAGGCTGCTG
                        agctaac  putative branch site (score: 2)
           aaaaataactagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctttgcctctctctctctctctctctctcacccacacacacactcacagaaaaataactagtagctaactctgtgaattggtgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCTTTTAAAGGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT