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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaaaatactatttagtatttacattattatagctgattactttattctaattttcactttgccctgttatctcatatgttttcctgtatgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATGTGCATTAACAAGAGCTACTATTTATAGCACCCCAATTGGGGATTTGCCA

Basic information

species Oryza sativa
transcript LOC_Os08g20270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g20270.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G016827_T04 (Zea mays), 3'ss of exon 1
caaaaaatactatt-tagta-tttacattattatagc-tgattactttattctaattttcactttgccc-tgttatctcatatgttttcctgtatgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATGTGCATTAACAAGAGCTACTATTTATAGCACCCCAATTGGGGATTTGCCA
    |||||  ||| |||||  || || |    || | | | || ||   |  ||  | | |  ||    || | |   ||   ||||| || |||| || |||||||||||| || ||| | |||||||| ||||||||||| |||||||||||||| ||||| || ||| || | ||  | |||||||| ||||||||||||
----aaatatcattctagtaactttcagtcggctatcataactatttctcttcaaaatgctcaatgttaatggtctgctattctttttcttgcatgtaattcagTTCTCGGGTGTTTCTGCTTGGCCCTTCTCATCACTACTACACTCCAAAATGTGCTTTAACCAGGGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCA
















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|88390884|gb|CI611110.1|CI611110
EST:     TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
EST: gi|88826685|gb|CI777250.1|CI777250
EST:     CAGGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: CAGGG-CGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
EST: gi|88288464|gb|CI661669.1|CI661669
EST:     TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
EST: gi|40486364|gb|BX897928.1|BX897928
EST:     TCAGGGCGGTGTGCGGTTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
EST: gi|88371235|gb|CI597712.1|CI597712
EST:     TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
EST: gi|66917040|gb|CX103888.1|CX103888
EST:     TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
EST: gi|33810210|gb|CF330996.1|CF330996
EST:     TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
EST: gi|58678103|gb|CK066790.1|CK066790
EST:     TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
EST: gi|88417210|gb|CI576284.1|CI576284
EST:     TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACAT                         TTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG
genomic: TCAGGGCGGTGTGCGGCTTATGCTTTTGGCAACATTGATCCAACTAACATgtatgttatt ... tgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctaattttcactttgccctgttatctcatatgttttcctgtatgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATGTGCATTAACAAGAGCTACTATTTATAGCACCCCAATTGGGGATTTGCCA
 ttctaat  putative branch site (score: 2)
                              atatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaaaatactatttagtatttacattattatagctgattactttattctaattttcactttgccctgttatctcatatgttttcctgtatgtgatccagTTCTCGGGTCTTCCTGTTAGGCCCTTCACATCACTACTATACTCCAAAATGTGCATTAACAAGAGCTACTATTTATAGCACCCCAATTGGGGATTTGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT