Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgtaaaactatttatgtatattactagtaattgagtatgtgcataatacaagacataacacaatacttagcccacttacatttatatcctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCAT

Basic information

species Oryza sativa
transcript LOC_Os05g38370.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 1
-atgtgtaaaactatttatgtatattactagtaattgagtatgtgcataatacaagacataacacaatacttagcccacttacatttatatcctttc-acagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCAT
 | |||   | |   |  |  ||||  | |  | || ||    || ||    | |   |   ||  | | |  |   ||||||  || || | | || | ||||||||| ||||| ||||| ||||| | ||||||||||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||| ||||||||
aaagtgagcacccgctgtttcatatcgccaagatttcagatactgtat--cccgaataaagtcatgaaaatatgaatacttaccattttaccttgtctatagTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCCATGAAGATAACTCTATTTTCTCATTTGAAATTGGACAAGGCGCTGTCAT

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 2
----atgtgtaaaactatttatgtatattactagtaattgagtatgtgcata-atacaagacataacacaatacttagcccacttacatttatatcctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCAT
     | |||| || |  ||    |||||| |  |  |   || | |    | || |  ||  | ||   || |||    ||   | |||  |||  ||   |||||||||||||||||||||| ||||| | |||||||||||| ||||| || |||||||| ||| | || ||||| || || |||||  | ||   ||| ||
aaggttctgtagaagtcattccaaatattaattatcttaaggtttatttgcatatgcttgattttac-tgattcttgtttca---atattgctatg-ttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTAT

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 2
atgtgtaaaactatttatgtatattactagtaattgag---tatgtgcataatacaagacataacac-aatacttagcccacttacatttatatcctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCAT-
 |  ||     |  | || || ||||   |   || ||   ||| | ||||| |      ||   ||  || |||    ||   | |||  |||  ||   |||||||||||||||||||||| ||||| | |||||||||||| ||||| || |||||||| ||| | || ||||| || || |||||  | ||   ||| || 
-taagttctgattctgatctaaattagatgagtttaaggtttatttacataaaatgcttgattttactgattcttgtttca---atattgctatg-ttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTATC

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|58653405|gb|CK042085.1|CK042085
EST:     AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATG                         TTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
genomic: AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATGgtactgcagt ... cctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
EST: gi|87012835|gb|CI297062.1|CI297062
EST:     AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATG                         TTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
genomic: AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATGgtactgcagt ... cctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
EST: gi|58670906|gb|CK059592.1|CK059592
EST:     AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATG                         TTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
genomic: AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATGgtactgcagt ... cctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
EST: gi|88382451|gb|CI633309.1|CI633309
EST:     AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATG                         TTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
genomic: AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATGgtactgcagt ... cctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
EST: gi|58676992|gb|CK065679.1|CK065679
EST:     AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATG                         TTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
genomic: AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATGgtactgcagt ... cctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
EST: gi|38477211|gb|CF961344.1|CF961344
EST:     AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATG                         TTCATTATGAAGGCACACTCGCTGAACATGGTGAAGTTTTCGACACCACTC
genomic: AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATGgtactgcagt ... cctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
EST: gi|88572905|gb|CI664476.1|CI664476
EST:     AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATG                         TTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC
genomic: AGCAAAGGATGATGCTATAGCTCCAACTGATAGTCTTCCCTTGGTTGATGgtactgcagt ... cctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatacaagacataacacaatacttagcccacttacatttatatcctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCAT
                              cacttac  putative branch site (score: 2)
                                          tatcctttc  putative PPT
                               acttacatttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgtaaaactatttatgtatattactagtaattgagtatgtgcataatacaagacataacacaatacttagcccacttacatttatatcctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT