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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag

Basic information

species Vitis vinifera
transcript Vv18s0001g08380.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g08380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os07g03770.1 (Oryza sativa), 5'ss of exon 4
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatatcctctttgacctgtatccta-cacttggtcaaactgttagaatgatctt-tacataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag
|||  |||||||||||||||||||||| || || || || || |||||||||||||| ||  | ||||||||| | |||||||| ||||| |||||||||||| |  ||  |      |  |   |  ||  |  | ||  || ||  | ||| | ||  | ||||       | | |   |||||  || |  |||   | |  | ||  ||  |     ||||| ||   | |      |  ||||   |||                    
AGAATTTTCCAAGAAAAAGAAGAAAGGAAAGCTGCCTAAGGAGGCCAGGCAGAAGCTGCTTCACTGGTGGGAGCTGCACTACAAGTGGCCTTACCCCTCAgtaagattacacatacaaaattacctgataatatatagt--aattgccacaattacctaatgcata------catagttctacaaa-catcttagtt--cagatcagatgcatcatcaca-ttgttactaacttt----gcaccaatgggatgagtag----------------

upper sequence: Vv18s0001g08380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g56110.2 (Oryza sativa), 5'ss of exon 4
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag
 | | | |||||||  |  ||||||||||| || ||||| || |||||||||||||| ||  | ||||||||| | |||||||| ||||| || ||||| ||| |||         |  || || |  |  | |    || | | |  | |  |  || ||      ||  ||| ||    ||| |      |||    |  |  |                                                                  
GGTGTTCTCCAAGAGGACCAAGAAAGGGAAGCTTCCCAAGGAGGCCAGGCAGAAGCTTCTGCACTGGTGGGAGCTGCACTACAAGTGGCCCTATCCCTCCgtacgcacgcatcacat--cccgtttgatcaattcaaccacattttctgcaccaaattaactcg---tttgaaaatgcgtgaaatttacggggttgtgtatgagcag-----------------------------------------------------------------

upper sequence: Vv18s0001g08380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g51690.3 (Oryza sativa), 5'ss of exon 3
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatg-catatcctctttgacctgtatcctacacttggtcaaactgttagaatgatcttt-acataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag
||| || || ||||| ||||| |||||||| || ||||| || ||  | ||  |||| ||||| ||||||||| | |||||||||||||| |||||||| ||| |    ||| ||||       | | | | | ||| ||  |   |    ||||      |     ||   |||||   |   |  | ||  | ||  || |                                                                       
AGAACTGTCAAAGAAGAAGAAAAAAGGGAAGCTCCCCAAGGATGCTCGTCAACAGCTCCTCAACTGGTGGGAGCTGCACTACAAATGGCCTTACCCCTCGgtaagattcatcatcttc--ttaattttccata-ttgatcttatgatctatatgactagggatgctgaacattaaatataagttacttcta-gttttggtacag----------------------------------------------------------------------

upper sequence: Vv18s0001g08380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G028041_T01 (Zea mays), 5'ss of exon 4
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttacta-aaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag
 ||| |||||||||| |||||||||||||| || || || || ||||||||||| || ||| | ||||||||| | |||||||| ||||| ||||| |||||| | |||| || | |||  | | || |||       || ||  | |   | || | || | | ||    |||    |    |   |  |||| |  | || |||  | |                                                              
GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaag-atatactatctgatatctctcatac-------catacattaatgctcatatgtataaagaac---aaacacaacgccatcgtccatgtcatgataagaatgataa--------------------------------------------------------------

upper sequence: Vv18s0001g08380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G452178_T01 (Zea mays), 5'ss of exon 4
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag
 ||| | |||||||| |||||||||||||| || || || || |||||||||||||| ||| | ||||||||| | |||||||| ||||| ||||| || ||  |            |||   | |||    |  || |   |  |||  |  ||  | ||| |    |     |    | | || |     ||  ||        |   | | | | |||||   |   |||  | ||                                 
GGAGTTCTCCAAGAAGAAGAAGAAAGGGAAGCTGCCGAAGGAGGCCAGGCAGAAGCTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCGgtgaga-----------gactaatctcccgtgc--ggccgtgcc-ttaacacaatgctgacagatcgattaccgtactcatacagcacgcgcgtgccttgtgcccttggctcgctgtgcttgtgtttg--tctgaacatgcag-----------------------------

upper sequence: Vv18s0001g08380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G135447_T01 (Zea mays), 5'ss of exon 4
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatg--catatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag
 ||| | |||||||  |||||||||||||| || ||||| || || ||||||||| | ||  | ||||||||| | |||||||| ||||| ||||| || ||| |  | || |    ||  | |  ||||     ||| | | ||      ||  | || |   ||   ||  ||   | || ||| |  |   | |  | |   ||   || |||||    |  ||                                               
GGAGTTCTCCAAGAGGAAGAAGAAAGGGAAGCTCCCCAAGGAGGCGAGGCAGAAGTTGCTGCACTGGTGGGAGCTGCACTACAAGTGGCCCTACCCTTCTgtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaacta-ctgtgtctatgtttggaagaagaaaaaaaatgaa---gcttttgatgcatgactactgtttcgagtactcaccag------------------------------------------

upper sequence: Vv18s0001g08380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G08150.1 (Arabidopsis thaliana), 5'ss of exon 4
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag
||| || |||||||| || |||||||| ||||| || ||||| ||  |||||||||| ||||  ||||||||||| || ||||| |||||||| || || ||| | |||   | | |  | | | || |   | |  |  |  | ||| |||      ||||   ||||     ||  || ||  ||| | |    |||  || |                                                                   
AGAACTATCCAAGAAGAAAAAGAAAGGTAAACTTCCTAAAGAAGCACGGCAGAAGCTTCTCACGTGGTGGGAGTTGCATTACAAGTGGCCATATCCTTCTgtacgtataaattttctctcatctctctttgccctcat--attttttaaaatatatactaca---aattaagtgttttaaaaacctatctttaa-gctagcaattc------------------------------------------------------------------

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|156737266|gb|EV241387.1|EV241387
EST:     AGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCA                         GAGACAGAGAAGGTGGCCTTGGCTGAAACTACTGGTTTGGACCAGAAACAA
genomic: AGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatat ... gatttcacagGAGACAGAGAAGGTGGCCTTGGCTGAAACTACTGGTTTGGACCAGAAACAA
EST: gi|34546295|gb|CF514527.1|CF514527
EST:     AGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCA                         GAGACAGAGAAGGTGGCCTTGGCTGAAACTACTGGTTTGGACCAGAAACAA
genomic: AGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatat ... gatttcacagGAGACAGAGAAGGTGGCCTTGGCTGAAACTACTGGTTTGGACCAGAAACAA
EST: gi|294964509|gb|GW838312.1|GW838312
EST:     AGAAGCTACTCAATGGGTGGGAGT-ACACTACAAATGGGCATACCC-TCA                         GAGACAGAGA-GGTGGC
genomic: AGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatat ... gatttcacagGAGACAGAGAAGGTGGC
EST: gi|110381205|gb|EC946526.1|EC946526
EST:     AGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCA                         GAGACAGAGAAGGTGGCCTTGGCTGAAACTACTGGTTTGGACCAGAAACAA
genomic: AGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatat ... gatttcacagGAGACAGAGAAGGTGGCCTTGGCTGAAACTACTGGTTTGGACCAGAAACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG