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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG

Basic information

species Vitis vinifera
transcript Vv10s0071g01060.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
---atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
    |||  | | |       | || ||| | |       |    |||   |  || |  |||   |     ||| ||||||   |    |     |||| ||||||| ||||||||||||||| | ||||||||||| || ||  | || || ||  | || ||||||||  |||||||||| ||||||||||| ||||| |
ttcgtgatga-tgataatacatatgaggtgcctggtaatttaccatgctggttatg-ttgctgtgcgtctaatttctttcttaacttt-ttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG

upper sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
--atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
  | |  | ||| |      |    || | ||  |    |        | | ||     |  |  ||| || |||  |   || |  | |     | | |||||||||||||||||||||||| | ||||| ||||| || ||  | ||||||||  | || ||||||||  |||||||||| ||||||||||| ||||| |
tgacgctacatttcca--cctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG

upper sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G008714_T01 (Zea mays), 3'ss of exon 2
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatg-tttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
 | | |    |    | |  |||   | |  ||    || |  |  ||  ||   |  | |  ||| || ||  |||| |  |   | |     | | |||||||| ||||||||||||||| | ||||| ||||| || ||  | ||||||||  | || ||||||||  |||||||||| ||||||||||| || || |
ttcatattacatcatgataatgtacatatagaacttatgatc-gtgttggttatgctgtcatggatctgattcctttcatgatatggtttccgctatgcagGTTGAAAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCTGTTG

upper sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcat-ttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttc---agGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
     |    |||   ||  | || ||  |  |  |   || | |   ||||||       | | | |  |  |  | | | ||    |||   | | |   |||||||||| || || || ||  | || || || |||||  | || ||||||||  | |||||||| || ||||||||||| ||||||||||||||||| |
----tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG

upper sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 2
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggt-cactgaatgatatgtttttttctttg---ttgagctgaaa-attttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
     | |||  | |        | | | |    |  ||||| |  ||| |   |   ||||| ||||    || |||| ||   ||  |||     ||||  |||||||||| || ||||| ||  | || || || |||||  | || ||||||||  | |||||||| || || |||||||| ||||||||||||||||| |
----tatattctttataacacaagttgcatgctagtttgtttggtttttttccatatgctgaa-gataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG

upper sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgttt---ttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
             |   |||     ||   |     | | || ||||||  ||   | |||   |||  | |   | || | | ||  | |   | |||  ||||||||||||| || ||||| || ||||| ||||| || || ||||| || ||  | |||||||||||||| ||||||||||| |||||||| ||  | |
-------------gtacttcaaaattttcacgtatggcgatt-gcattttatgtatattgaggtataaatctgactcttttctctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG

upper sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
 |   || ||||  |  || | |   |  |     |     |||  |||   |||       ||||  |  ||||| | |             | || |||||||||||||||| || ||  | || |||||||| || || ||||| |||||  | ||||||||||| || |||||||| || |||||||| ||  | |
gtacaaagttac--accttatttcacttgtggctaaag---ttggttttaaaggtaggattgtgattagaatttttatct-------------tattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG

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|161717015|gb|FC066535.1|FC066535
EST:     TTCGTAAGGTGCTCGGATCCCATGCTAAGCGTATACAGTTAATGTCAAAG                         GTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACT
genomic: TTCGTAAGGTGCTCGGATCCCATGCTAAGCGTATACAGTTAATGTCAAAGgtatgtggat ... aaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACT
EST: gi|161712166|gb|FC061538.1|FC061538
EST:     TTCGTAAGGTGCTCGGATCCCATGCTAAGCGTATACAGTTAATGTCAAAG                         GTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACT
genomic: TTCGTAAGGTGCTCGGATCCCATGCTAAGCGTATACAGTTAATGTCAAAGgtatgtggat ... aaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACT
EST: gi|161711988|gb|FC059580.1|FC059580
EST:     TTCGTAAGGTGCTCGGATCCCATGCTAAGCGTATACAGTTAATGTCAAAG                         GTTGAGAACCAAGAGGGT
genomic: TTCGTAAGGTGCTCGGATCCCATGCTAAGCGTATACAGTTAATGTCAAAGgtatgtggat ... aaattttcagGTTGAGAACCAAGAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
                                                ttttc  CT-rich tract
               aatgatatgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- -agaaatt
- - - - - - - - - - - - - - - - - - - - - -gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatg