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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcactatcttttcatttttcctgagtgtccaggcattcgcatttttttgtcacaaggtaacaatagtgcctctgccttgtatccagGTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCTATAACTCTTTCCCCTGAAGAGTTTTTCCCTCAGTGGAAAGCATTGAATG

Basic information

species Oryza sativa
transcript LOC_Os03g02150.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 22
gtaagtgcactatcttttcatttttcc----tgagtgtccaggcattcgcatttttttgtcacaaggtaacaatagtgcctctgccttg--tatccagGTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCTATAACTCTTTCCCCTGAAGAGTTTTTCCCTCAGTGGAAAGCATTGAATG
|| | |   |||     |||| |||||    | ||||||     |||| | | || |||||||  ||||| |||  ||    ||  |||  ||| |||||| ||| |||||| || |||||||||||||||||||||||||||||  ||||||||||| |||||||||| |||||| | |||||||||||  | | ||
gtgattattctacgccatcatatttcccccctaagtgtctgaatattcacctattattgtcacctggtaataatgctgttcttgttttgcttatgcagGTGGATGCCAAACTTCGACTCCCTGTTGTATTGAATAAATTTTTGCAGACTATAACTCTTACCCCTGAAGAATTTTTCTCCCAGTGGAAAGCGCTTACTG

upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G092741_T01 (Zea mays), 3'ss of exon 7
gtaagtgcactatct--tttcatttttcc--tgagtgtccaggcattcgcatttttttgtcacaaggtaacaatagtgcctctgccttg--tatccagGTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCTATAACTCTTTCCCCTGAAGAGTTTTTCCCTCAGTGGAAAGCATTGAATG
|| | |   |||| |  ||  ||||||||  ||||||||     |||| | | | |||||  | ||||||||||   | || ||  |||  ||| |||||| ||| |||||| || || |||||||||||||||||||||||||| |||||||||||| |||||||||| |||||||  |||||||||||  ||| ||
gtgattattctatgtcattgtatttttcccctgagtgtctgaatattcacttgtctttgttgccaggtaacaatgtcgtctttgttttgcttatgcagGTGGATGGCAAACTTCGACTTCCTGTTGTATTGAATAAATTTTTGCAGCCTATAACTCTTACCCCTGAAGAATTTTTCCTCCAGTGGAAAGCGCTGACTG
















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|32948119|gb|BP184691.1|BP184691
EST:     GTAGAGATGTCGCTGTTCTTGATTTTTCATATACATTTGGAACTTCACTG                         GTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCT
genomic: GTAGAGATGTCGCTGTTCTTGATTTTTCATATACATTTGGAACTTCACTGgtaagtgcac ... ttgtatccagGTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCT
EST: gi|58686104|gb|CK074791.1|CK074791
EST:     GTAGAGATGTCGCTGTTCTTGATTCTACATATACATTTGGAACTTCACTG                         GTGAATGTCAAACTCCGGCTCC
genomic: GTAGAGATGTCGCTGTTCTTGATTTTTCATATACATTTGGAACTTCACTGgtaagtgcac ... ttgtatccagGTGAATGTCAAACTCCGGCTCC
EST: gi|163923306|gb|EG709361.1|EG709361
EST:     GTAGAGATGTCGCTGTTCTTGATTTTTCATATACATTTGGAACTTCACTG                         GTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCT
genomic: GTAGAGATGTCGCTGTTCTTGATTTTTCATATACATTTGGAACTTCACTGgtaagtgcac ... ttgtatccagGTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCT
EST: gi|66918984|gb|CX105832.1|CX105832
EST:     GTAGAGATGTCGCTGTTCTTGATTTTTCATATACATTTGGAACTTCACTG                         GTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCT
genomic: GTAGAGATGTCGCTGTTCTTGATTTTTCATATACATTTGGAACTTCACTGgtaagtgcac ... ttgtatccagGTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcattcgcatttttttgtcacaaggtaacaatagtgcctctgccttgtatccagGTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCTATAACTCTTTCCCCTGAAGAGTTTTTCCCTCAGTGGAAAGCATTGAATG
                       aggtaac  putative branch site (score: 3)
                                     cctctgcctt  putative PPT
         atttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcactatcttttcatttttcctgagtgtccaggcattcgcatttttttgtcacaaggtaacaatagtgcctctgccttgtatccagGTGAATGTCAAACTCCGGCTCCCTGTTGTATTGAATAAATTTTTGCAACCTATAACTCTTTCCCCTGAAGAGTTTTTCCCTCAGTGGAAAGCATTGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA