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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTCAACACCTGACAAAAGAGGATTTAAGCAAGTTATTTTTTGGGGAGTTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagttttccttttctttttttccctttcttctcatttcctttccactagtttaaaaataataatgggtctgggttgagggacctgattgattgcctt...

Basic information

species Vitis vinifera
transcript Vv10s0116g01540.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g01540.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA07G39190.1 (Glycine max), 5'ss of exon 3
TTCTTCAACACCTGACAAAAGAGGATTTAAGCAAGTTATTTTTTGGGGAGTTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagttttccttttctttt-tttccctttcttctcatttcctttccactagtttaaaaataataatgggtctgggttgagggacctgattgattgcctt------------------------------------------------------------------------------
||||||||||||| |||||||||||||| |||||| |||| |||||||||||||   | ||||| ||||| ||  ||   |||||||| ||  |||||||||||  ||||  | |  |||| |||| |   | || | | |   |||  | |  || |    | | |||   ||   |   |  |     || ||| | ||                                                                              
TTCTTCAACACCTAACAAAAGAGGATTTGAGCAAGCTATTCTTTGGGGAGTTCCGTGTGTTGGACATCAATGGCTCACAGTGCTTTCTTACCCGGACAGGgtatgcttttattgtcattttctttcaccaacatcacctatttattcttcaaagttcatccgagttatgaaactccatcttgt-attactttaatttcattattgaatgtttgtgttatgagctcagagtttcttagggataccatgcataataacactttcttgattgagactttcag

upper sequence: Vv10s0116g01540.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA15G11590.1 (Glycine max), 5'ss of exon 3
TTCTTCAACACCTGACAAAAGAGGATTTAAGCAAGTTATTTTTTGGGGAGTTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagttttccttttctttttttccctttcttc--tcatttcctttcca---ctagtttaaaa-ataataatgggtctgggttgagggacctgattgattgcctt
||||||||||||||||||||||||||||||||||| | |  |||||||||||||   | ||||| ||||| || |     |||||||||||  | |||||||||  |||  | |   ||  |||   || | |     |||| | ||  |   || || | | |  || |||||   |  |  |      | ||  || |      
TTCTTCAACACCTGACAAAAGAGGATTTAAGCAAGATGTACTTTGGGGAGTTCCGTGTGTTGGACATCAATGGTGTGCAGTGCTTTCTCACACGAACAGGgtatgttttcacgtggtttgctttatgttacattagcaatttaccttgtaaatctcgtctgagatgtagtaatgctacctgaatttccatcttgtatggt------

upper sequence: Vv10s0116g01540.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA17G01550.1 (Glycine max), 5'ss of exon 3
TTCTTCAACACCTGACAAAAGAGGATTTAAGCAAGTTATTTTTTGGGGAGTTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagttttccttttctttttttcc--ctttcttctcatttcctttccactagtttaaaaataataatgggtctgggttgagggacctgattgattgcctt
|||||||||||||||||||||||||||| |||||| | |  |||||||||||||   | ||||| ||||| ||  ||   || ||||| || ||||||||||||  ||||| | |  |||| ||||  |    |   || ||  ||    | ||||   |||    |    || |   ||  |  | |  ||   || ||||
TTCTTCAACACCTGACAAAAGAGGATTTGAGCAAGCTCTACTTTGGGGAGTTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgcttttcttgtcattttcttccaccaacatcaccaatttattcatccgagttatgaaactccatcttgtattactttggctatc--atgcctttcctt

upper sequence: Vv10s0116g01540.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G00710.1 (Glycine max), 5'ss of exon 3
TTCTTCAACACCTGACAAAAGAGGATTTAAGCAAGTTATTTTTTGGGGAGTTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagttttccttttctttttttccctttc-ttctcatttcctttccactagttt-----aaaaataataatgggtctgggttgagggacctgattgattgcctt
|||||||||||||||||||||  |||||||||||| | |  |||||||  |||||| | ||||| ||||| || |     |||||||||||  |||||||||||  |||    ||  ||  ||||  |  | ||  || |||   |     |||||     | |  || |||||   |  |  |      | |   ||||      
TTCTTCAACACCTGACAAAAGCAGATTTAAGCAAGATGTACTTTGGGGGTTTCCAAGTGTTGGACATCAATGGTGTGCAGTGCTTTCTCACACGGACAGGgtatgttttcatgttgtttgctttctgtaacattagcaattcaacttgtaaagtttgtctgagatgtagtaatgttacctgaatttccatcttatatgat------

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|34549398|gb|CF517630.1|CF517630
EST:     TCCAAATCTTGGATATCAACGGAGGATCGAT-CNTTCTCACTAGGACAGG                         GTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
genomic: TCCAAATCTTGGATATCAACGGAGCAAC-CTGCTTTCTCACTAGGACAGGgtatagtttt ... aaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
EST: gi|29784997|gb|CB341605.2|CB341605
EST:     TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGG                         GTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
genomic: TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagtttt ... aaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
EST: gi|294965088|gb|GW838891.1|GW838891
EST:     TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGG                         GTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAAAATGCAGT
genomic: TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagtttt ... aaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
EST: gi|28959313|gb|CB339657.1|CB339657
EST:     TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGG                         GTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
genomic: TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagtttt ... aaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
EST: gi|34545207|gb|CF513439.1|CF513439
EST:     TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGG                         GTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
genomic: TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagtttt ... aaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
EST: gi|34546202|gb|CF514434.1|CF514434
EST:     TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGG                         GTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
genomic: TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagtttt ... aaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
EST: gi|110379781|gb|EC945000.1|EC945000
EST:     TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGG                         GTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
genomic: TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagtttt ... aaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
EST: gi|29785120|gb|CB341857.2|CB341857
EST:     TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGG                         GTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT
genomic: TTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagtttt ... aaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTTCAACACCTGACAAAAGAGGATTTAAGCAAGTTATTTTTTGGGGAGTTCCAAATCTTGGATATCAACGGAGCAACCTGCTTTCTCACTAGGACAGGgtatagttttccttttctttttttccctttcttctcatttcctttccactagtttaaaaataataatgggtctgggttgagggacctgattgattgcctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa