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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcgtgcacacacagagatggattgagtaatatcccctttaaatgtgttatttctgtcactttcatgtgaattgtgtatatcctctttgttggtgacagAAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCGTTACTGAAGGATCAGGCAAAGTCTGATGACATTCTAAAAGCTGCTTTCC

Basic information

species Vitis vinifera
transcript Vv12s0035g01870.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
-----------------gtgcgtgcacacacagagatggattgagtaatatcccctttaaatgtgttatttctgtcactttcatgtgaattgtgtatatcctctttgttggtgacagAAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCGTTACTGAAGGATCAGGCAAAGTCTGATGACATTCTAAAAGCTGCTTTCC
                 |   | |      |||   |   || | | |  | |   || |   |||||| |    || | | |||| | ||||||   ||   |   ||| | |||||  ||||||||| | || |||||||| || || ||    || || |||||| | || ||||||||||||||||| ||||||||||| ||||| || ||||
gtaagcctttcttgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgt---tctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
















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|30304025|gb|CB980819.1|CB980819
EST:     ATGCTTTCCAAGATGCTGATTCATATCTCTCCATAGAGCCTCTGTTTGAG                         A--GAG-G-TATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCG
genomic: ATGCTTTCCAAGATGCTGGTTCATATCTCTCCATAGAGCCTCTGTTTGAGgtatactcct ... ttggtgacagAAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCG
EST: gi|110711704|gb|EE088489.1|EE088489
EST:     ATGCTTTCCAAGATGCTGGTTCATATCTCTCCATAGAGCCTCTGTTTGAG                         AAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCG
genomic: ATGCTTTCCAAGATGCTGGTTCATATCTCTCCATAGAGCCTCTGTTTGAGgtatactcct ... ttggtgacagAAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCG
EST: gi|161717211|gb|FC067217.1|FC067217
EST:     ATGCTTTCCAAGATGCTGGTTCATATCTCTCCATAGAGCCTCTGTTTGAG                         AAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCG
genomic: ATGCTTTCCAAGATGCTGGTTCATATCTCTCCATAGAGCCTCTGTTTGAGgtatactcct ... ttggtgacagAAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttatttctgtcactttcatgtgaattgtgtatatcctctttgttggtgacagAAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCGTTACTGAAGGATCAGGCAAAGTCTGATGACATTCTAAAAGCTGCTTTCC
                                    tcctctttgtt  CT-rich tract
                              tgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgcacacacagagatggattgagtaatatcccctttaaatgtgttatttctgtcactttcatgtgaattgtgtatatcctctttgttggtgacagAAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCGTTACTGAAGGATCAGGCAAAGTCTGATGACATTCTAAAAGCTGCTTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-tgcgtgc
- - - - acacaca
- - - - - - - - - -tggattg
- - - - - - - - - - - - - - - - -tcccctt