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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actcatttttatcttttcaactttctttctcatcaatattgtttcttatttctgttcctggagtaataattgtaatatcatgcttctacgttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAGGGACAAGAATTCAACTTCACTATTAAAAGAGGAGTCAGCTCAGAAAACA

Basic information

species Vitis vinifera
transcript Vv02s0012g01170.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 2
actcatttttatcttttcaactttctttctcatcaatattgtttcttatttctgttcctggagtaat--aattgtaat-atcatgcttctacgttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAGGGACAAGAATTCAACTTCACTATTAAAAGAGGAGTCAGCTCAGAAAACA
                     | |  | |   | || |     |   ||||    | ||| || ||   |  ||| || |||   ||||   | |     |||||||| || || |||||||| ||||| ||  |||||||||||||  |||| || ||||| ||||| || |||||||||||||| || ||| |  || |||
--------------------gtatactgccgttgaacaca---tgaaattttgaatgctgcagcaaatgagctgtgatgatcgaacttcagtgatg----cagGGTCCAGAAGTGAGAAGTGGGGATGTTCCAGAACCAATCATGCTCGAGGAAGGTCAAGAGTTCAATTTTACTATTAAAAGAGGGGTGAGCACCAAAGACA

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 2
actcatttttatcttttcaactttctttctcatcaatattgtttcttatttctgttcctggagtaataattgtaatatcatgcttctacgttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAGGGACAAGAATTCAACTTCACTATTAAAAGAGGAGTCAGCTCAGAAAACA
                       | | ||||| |   ||   |    | |  |  | |   |     |||| | ||  |    ||  | |       ||||||||||| || |||||||| ||||| ||  | ||||||||||| ||||| || ||||| ||||||||||| ||||||||||| || ||| | ||| |||
----------------------gtatatctcagctgcatacatcaaaactaattctacaacaacttaaattcttatgactgagtttgatggatg---cagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATCATGCTCAAGGAAGGTCAAGAGTTCAACTTCACGATTAAAAGAGGGGTGAGCACTGAAGACA

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G033526_T03 (Zea mays), 3'ss of exon 2
actcatttttatcttttcaactttctttctcatcaatattgtttcttatttctgttcctggagtaataattgtaatatcatgcttctacgttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAGGGACAAGAATTCAACTTCACTATTAAAAGAGGAGTCAGCTCAGAAAACA
                       | | ||||| |   ||   |    | |  |  | |   |     |||| | ||  |    ||  | |       ||||||||||| || |||||||| ||||| ||  | ||||||||||| ||||| || ||||| ||||||||||| ||||||||||| || ||| |        
----------------------gtatatctcagctgcatacatcaaaactaattctacaacaacttaaattcttatgactgagtttgatggatg---cagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATCATGCTCAAGGAAGGTCAAGAGTTCAACTTCACGATTAAAAGAGGGGTGAGCAC--------

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|71857948|gb|DT007003.1|DT007003
EST:     ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAG                         GGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
genomic: ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAGgtatgctggt ... ttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
EST: gi|351025070|gb|FQ433487.1|FQ433487
EST:     ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAG                         GGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
genomic: ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAGgtatgctggt ... ttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
EST: gi|351014767|gb|FQ437967.1|FQ437967
EST:     ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAG                         GGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
genomic: ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAGgtatgctggt ... ttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
EST: gi|351030123|gb|FQ430865.1|FQ430865
EST:     ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAG                         GGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
genomic: ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAGgtatgctggt ... ttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
EST: gi|37184317|gb|CF603671.1|CF603671
EST:     ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAG                         GGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
genomic: ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAGgtatgctggt ... ttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
EST: gi|351027131|gb|FQ439993.1|FQ439993
EST:     ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAG                         GGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG
genomic: ACAATGCTCAATTTGAAGACAAGGTTATAGCCATAATGCTGGACACCAAGgtatgctggt ... ttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttctgttcctggagtaataattgtaatatcatgcttctacgttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAGGGACAAGAATTCAACTTCACTATTAAAAGAGGAGTCAGCTCAGAAAACA
                                     cttctacgttcttccc  CT-rich tract
                  taataattgtaatatc  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actcatttttatcttttcaactttctttctcatcaatattgtttcttatttctgttcctggagtaataattgtaatatcatgcttctacgttcttcccagGGTCCTGAGGTCAGAAGTGGAGATGTCCCTAAACCAATCATGCTTAAGGAGGGACAAGAATTCAACTTCACTATTAAAAGAGGAGTCAGCTCAGAAAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - ctcatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct