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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttggtgtcacatgcttatgaaggctttttataattgttgattatgcagttaagtaagttccttgttcacccttttctgtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG

Basic information

species Vitis vinifera
transcript Vv12s0057g01480.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 6
gtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttgg----tgtcacatgcttatgaaggctttttataattgtt-gatt-atgcagtta-agtaagtt--ccttgttcacccttttctgtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG
||||||    ||    |   |||  |||  || | || |  |||  ||     | |   || ||||  || | | |  |  ||  |  |||| ||  | ||| || ||  |  | ||||   || | || ||| |    ||||||| ||||| || ||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||  |||| ||||| ||||||||||| |||
gtaagtatttcagaaccttcacat-tctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttc-catagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAAGGTGCAATTATTGAAGACACGTTATTAATGGGGGCAGATTATTACGAG

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 6
gtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttgg----tgtcacatgcttatgaaggctttttataattgtt-gatta-tgcagtta-agtaagtt--ccttgttcacccttttctgtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG
|||||     ||    |   |||  |||  || | || |   ||  ||     | |   || ||||  || | | |  |  ||  |  ||||| |  | ||| || ||  |  ||||||   || |  | |||||    ||||||| ||||| || ||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||  |||| ||||| ||||||||||| |||
gtaagcatttcagaaccttcacat-tctactgatctgctctgtacatgagatttatacaattcttaacaaagatgtcaaatataatgagattaatttatttataggaaactaaccttgtattccatactttgtgc-catagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAAGGTGCAATTATTGAAGACACGTTATTAATGGGGGCAGATTATTACGAG

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttggtgtcacatgcttatgaaggctttttataattgttgattatgcagttaagtaagttccttgttcaccctttt-ctgtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG
                                                       |   | |  |  |||| |  |   | |    | | | |  |    | |||     |  |   |    | ||    |||||||| ||||| ||||| |||||||| || ||||| || ||||||||||| ||||| ||||| |||||| |  |||| |||||||| |||||||| |||
-----------------------------------------------------gtacaatca-aatcgcttctgttcgatatatgctttacggacatacgaattcaccaatgtcttatgaattttgggcacagAACTGCAAAATTCATCACTCTGTGGTTGGACTCCGTTCCTGCATATCAGAAGGTGCTATTATTGAAGATTCGTTATTAATGGGAGCTGATTATTACGAG

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|33409675|gb|CF215302.1|CF215302
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|110688952|gb|EE068088.1|EE068088
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|110423492|gb|EC989838.1|EC989838
EST:     TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|161718175|gb|FC065663.1|FC065663
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTACGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|110378789|gb|EC943937.1|EC943937
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|352777901|gb|FQ466954.1|FQ466954
EST:     TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|71889085|gb|DT038140.1|DT038140
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|352776770|gb|FQ472657.1|FQ472657
EST:     TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|32245488|gb|CD711307.1|CD711307
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|83275545|gb|DV939553.1|DV939553
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|32245967|gb|CD711786.1|CD711786
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|33403137|gb|CF208764.1|CF208764
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
EST: gi|30253354|gb|CB970905.1|CB970905
EST:     TTGATGCTGATGTGACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAG                         AACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG
genomic: TTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttaca ... gtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttgattatgcagttaagtaagttccttgttcacccttttctgtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG
  tgttgat  putative branch site (score: 4)
                         ttccttgttcaccctt  putative PPT
                ttaagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttggtgtcacatgcttatgaaggctttttataattgttgattatgcagttaagtaagttccttgttcacccttttctgtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT