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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcgattaccttctcaaactccataactatatatatatatatatatatatatatatatatatatatatttatacatatgcttgtcctctgcataacacgtatatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGAGACAAGGGAAAATTTCCA

Basic information

species Vitis vinifera
transcript Vv08s0040g02650.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g38680.1 (Oryza sativa), 3'ss of exon 2
gtcagcgattaccttctcaaactccataactatatatatatatatatatatatatatatatatatatatatttatacatatgcttgtcctctgcataacacgtatatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGAGACAAGGGAAAATTTCCA
                              ||||| |  || | | |||   ||| ||| |    | | |       | |||     | | ||||| |     | ||  || |  |||||  ||     ||||| ||||||||  ||||||| ||||||||||||||||||||| |||||   |||  ||| | ||   |       ||   |||||| | | |     ||||
------------------------------tatattttaatctttgtatggctatgtatcttatgacagaagc-cggagatgtaatccatttgcattatctaaaaatatattttgatctttgtggcg--gcagTATGGAAGGAGCTGGAGAAGGAGAACAAGGAGTTCTTCGAGACCTACAACAAGGACAGGGCGGAGCGCAACATCGAGGCGGAGACGATGCAGCGGATCCA

upper sequence: Vv08s0040g02650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G108723_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------gtcagcgattaccttctcaaactccataactatatatatatatat-atatata-tatatatatata------tatatatt-tatacatatgcttgtcctctg-cataacacgta-tatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGAGACAAGGGAAAATTTCCA
                                            || |  | || ||||| |    || |  | |     | ||  |   ||  ||| |||   |  |||       ||| ||| |||   | |  || |  |||  |||  || ||  | || | |   |          | |||||||||||||||  | ||||||||||||||||||||||||||| | |||   |||  | | ||||   |       ||   |||||| | ||      || |
gtaccggccgtactaccgtgcatatatactggacacgcgcacgcgtta-tgctttccttcccccgttcaaccatttctcgtttaccttccatgcataatatgcttcaataatcgatcatagattatattgttgttgttctattctatcatttcatgtggtctgaaaaagcacaccacatgca-tgcagTGTGGAAGGAGCTAGAGAAAGAGAACAAGGAGTTCTTCGAGACGTACAACAAGGACCGCGAGGAGCGGAAGGTGGAGGCGGAGACGATGGCGCGGATCGA

upper sequence: Vv08s0040g02650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G370044_T01 (Zea mays), 3'ss of exon 2
--------------------------gtcagcgattaccttctcaaactccataactatatatatatatatatatatatatatatatatatatatatt-----------tatacatatgcttgtcctctgcataacacgtatatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGA-GACAAGGGAAAATTTCCA
                          |  ||||||||         | | ||  | ||  ||  |     |  |     |  || |  ||    || |           |||  || |  ||| ||||| | |  ||    ||| | |||| ||   | || ||  ||||||||||||||  ||||||| ||||||| ||||||||||||| | |||   |||      | | ||||||     | |   || ||         ||   ||
gtaggccgtaggcggcactcttgcaagcaagcgattaatcgagattatttcaagagtagttaagttgtcgtccacgccaaattaaagctactactagtcgactcgatcgtatcgatctcattgacctcttcttggcattattatac-tatacat---gctgctatagcagTGTGGAAGGAGCTGGAGAAGGAGAACAGGGAGTTCTTCGAGACGTACAAGAAGTATCTGG-GACAAGAGTCGGCGCTGCAGAAGAATCCATCCGATGGACA

upper sequence: Vv08s0040g02650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
gtcagcgattaccttctcaaactccataactatatatatatatatatatatatatatatatatatatatatttatacatatgcttgtcctctgcataacacgtatatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGAGACAAGGGAAAATTTCCA
                               || |   || |   || | | | |  || | | | | | | | |   | |  || | || |   | |     | | |   ||  || |    |     ||||| |||||||| || ||||| ||||||||||||||||||||| | ||| | | ||||||||  |  |||| ||| || |  ||||||||| |||   ||||
-------------------------------atgttgttaaagtaatgtgt-tgtcaatgttt-tctctctctctctctttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA

upper sequence: Vv08s0040g02650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G33110.1 (Glycine max), 3'ss of exon 2
gtcagcgattaccttctcaaactccataactatatatatatatatatatatatatatatatatatatatatttatacatatgcttgtcctctgcataacacgtatatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGAGACAAGGGAAAATTTCCA
                | | |     | | | | |     | | | | | | || |  ||||||||||||| | |   | ||         || || ||||  |  |||||  || |   |||| | | ||||| |||||||| || ||||| ||||||||||||||||||||| | ||| | | ||||||||  |  | || ||| || |  ||||||||| |||   ||||
----------------taatatgttgtcattgttttctcttttttttttctgta-acctatatatatatatgtgtgtgtgtg---------tgaatgacac--acgtgcatgcatgt---gatg-tgc-gcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGTAGAGAAAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA

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|22012300|gb|BQ797334.1|BQ797334
EST:     GGAAGCCCTCTCCAAACATGCTGACATCAAACCAGTCATCACTTCCACAG                         TGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAA
genomic: GGAAGCCCTCTCCAAACATGCTGACATCAAACCAGTCATCACTTCCACAGgtcagcgatt ... gatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAA
EST: gi|110422937|gb|EC989271.1|EC989271
EST:     GGAAGCCCTCTCCAAACATGCTGACATCAAACCAGTCATCACTTCCACAG                         TGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAA
genomic: GGAAGCCCTCTCCAAACATGCTGACATCAAACCAGTCATCACTTCCACAGgtcagcgatt ... gatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcttgtcctctgcataacacgtatatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGAGACAAGGGAAAATTTCCA
                        tatatgcatatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagcgattaccttctcaaactccataactatatatatatatatatatatatatatatatatatatatatttatacatatgcttgtcctctgcataacacgtatatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGAGACAAGGGAAAATTTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA