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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgtaattggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG

Basic information

species Vitis vinifera
transcript Vv08s0040g01700.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgtaattggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG
|| ||   | || ||    || | ||  ||||  | |   |    | |    |  | | ||    |||| || |        |||||| ||| | ||||| || |||||| | ||||| || ||||| || || ||||| || ||||| |||||||| || ||||||||||||||| ||||  | |
gtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattct--------ccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 2
gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgtaattgg-tgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG
    ||   |||||  |  ||||| ||| | |   |  |   || ||| |  |  ||| | |    |||    |  |||| |  ||||| ||| |||||||||| ||||| |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||||||||||||| | ||||||||||
----gtaaatttcacaacaattta-tgcacgtactatcat--ctgaattctgatcaatataatttgtttagcatttttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 2
gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgta-attggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG
    ||   |||||  |  ||| |     |||   |  | |  ||||| |  |  ||| | |    |||    |  || |||  ||||| ||| ||||||| || ||||| |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||||||||||||| | ||||||||||
----gtaaatttcacaacaattgatgttacatactatcatt--ttaattctgatcaatataatttgtttagcatttatgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgc-atagaaatttgaaggatttcttgtaattggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG
             | |||   ||    ||  |||| | | |  |    | ||||  | || | |  ||   ||      | || ||       |   |||| ||  ||||||| || ||||| || ||||| ||||| |||||||| |||||||| || || |||||||| |||| |||||||||||| ||||||||||
gtttagtttgttttaagtctattgatcgaatatttcaggttagttcttctaataaatgattctaatgatggttttgttttctcctgacgcatataatagGTTGTTAGAGGTGTGGTGGAAAGTCTTAAAATCATTACCCGTCAGGCGAGTTTGAGAGTTGCAGAGTATGCTTTTCTCTATGCCAAGACTCATGGAAGAG

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagt-tgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgtaattggt-gccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG
|| ||| | || |   |    |||| ||    | |  | | ||     |  | ||  || |  | ||||| |  |  ||  | || |||| ||    |||||||| ||||| || ||||| ||||| ||| |||| ||| |||| || || |||||||| ||||  ||||||||||| || |||||  
gttagtctattgttctgtcattttagtgaatctgtatctagtatcatttttagagccatgttgatgatttgtcatttttatttgctagGTCGTCAAGGGTGTAGTGGAAAGTCTTAAAATTATTACCCGTAAGGCGAGTATGAGAGTTGCCGAGTATGCCTTTCTTTATGCCAAGACTCACGGAAGGA

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|110685854|gb|EE062936.1|EE062936
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|110687099|gb|EE064211.1|EE064211
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|71860684|gb|DT009739.1|DT009739
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|33406750|gb|CF212377.1|CF212377
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTCGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|110723902|gb|EE099271.1|EE099271
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|351019648|gb|FQ439465.1|FQ439465
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|110712688|gb|EE087955.1|EE087955
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|161716798|gb|FC067212.1|FC067212
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|27585749|gb|CB008444.1|CB008444
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
EST: gi|71869279|gb|DT018334.1|DT018334
EST:     TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAA                         GTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT
genomic: TCACTATCCGTGAAAACACAGAAGGGGAGTACAGTGGACTTGAACATCAAgtgagttgtt ... ttggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgacaaatacttaatgcatagaaatttgaaggatttcttgtaattggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG
      aaatacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgtaattggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA