Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCAAGCTGCTTTTATATTGAGTATACCCAAGAGAAAATTGATGGACGAGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatacatgactaattcctgtgtacattgtttttcttcacagttctctctaaccagaccattcaacttacatttcttgttcaagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtag

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 16
TGACCAAGCTGCTTTTATATTGAGTATACCCAAGAGAAAATTGATGGACGAGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatacatgacta-attcctgtgtacattgtttttcttcacagttctctctaac-cagaccattcaacttacatttcttgttcaagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtag
 || ||||||||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||  | ||   |  || | ||    |  |||||    ||||    |  | ||||   ||| |   ||  |  || | |||                                                          
CGATCAAGCTGCTTTCATATTGAGTATACCTAAAAGAAAGTTAATGGATGAGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtatgatcatatatttgtatccttgaccgcgctgtttcaaatcac----ccatttaacgtcgacaaaataatctggatcttttgcag-------------------------------------------------------

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 16
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 15
TGACCAAGCTGCTTTTATATTGAGTATACCCAAGAGAAAATTGATGGACGAGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatacatgactaattcctgtgtacattgtttttcttcacagttctctctaaccagaccattcaacttacatttcttgttcaagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtag
 || ||||| || ||| |  ||||| | ||    || |||      || || || ||||||||  |  | |||||||||||||||||||  |||||||||||| |     |||    |||   | ||  | ||     |   |   || |   |   |  | |  |   | |  |||| ||| |||  ||  || ||  |    | |     |   |    ||| |              
GGATCAAGCAGCCTTTGTCCTGAGTGTGCCTCGAAGGAAACCAGCCGATGAAACTCAAGAAACATTGCGTACATCTGCTTTTCCAAGCACTCATGTGAAGgtatg---ctatggtcgatttgcgcgtcgaatg-----caaaaatattgtaggttgtcgtatcgattcccgttaattttttggtca--cgataattctgtactgaattggttcgcattatttacag--------------
















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|29676349|gb|CB672624.1|CB672624
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|218502457|gb|FG966789.1|FG966789
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|88691408|gb|CI733486.1|CI733486
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|88228655|gb|CI228135.1|CI228135
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|218479830|gb|FG949479.1|FG949479
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|66925445|gb|CX112293.1|CX112293
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|86477548|gb|CI120181.1|CI120181
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|29676347|gb|CB672622.1|CB672622
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|87022158|gb|CI259230.1|CI259230
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|86415053|gb|CI069456.1|CI069456
EST:     CAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTTCATTGCTTCGATATGCTATGGCCGGACA
genomic: CAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|29685518|gb|CB681793.1|CB681793
EST:     CTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: CTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|32948151|gb|BP184723.1|BP184723
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|29623308|gb|CB628319.1|CB628319
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|4714663|gb|AU055780.1|AU055780
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGAC
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAA-Ggtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGAC
EST: gi|163918227|gb|EG714811.1|EG714811
EST:     CTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTGGATATGCTATGGCCGGACA
genomic: CTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|88691475|gb|CI733553.1|CI733553
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|87022798|gb|CI269734.1|CI269734
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|29629025|gb|CB634036.1|CB634036
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|88691488|gb|CI733566.1|CI733566
EST:     AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
EST: gi|58678949|gb|CK067636.1|CK067636
EST:     AGACGCAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAG                         GAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA
genomic: AGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatac ... ctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACCAAGCTGCTTTTATATTGAGTATACCCAAGAGAAAATTGATGGACGAGACACAAGAAACTCTTAGAACATCTGCTTTTCCAAGCAACCATGTGAAGgtacgaatacatgactaattcctgtgtacattgtttttcttcacagttctctctaaccagaccattcaacttacatttcttgttcaagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA