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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcagagttttgattgagtggaatgacatgtttatgctgcctgcattatggatatgccgactagttattgattcttttttttttttttttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAAGCATTTAGTGGGAAGAGCTACTCCTTGAAACGTTAGCTGGATTTTGTAG

Basic information

species Oryza sativa
transcript LOC_Os04g48770.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G114220_T01 (Zea mays), 3'ss of exon 9
tgagcagagttttgattgagtggaatgacatgtttatgct--gcctgcattatggatatgccgactagttat-tgattcttttttttttt------tttttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGA---GCCCAAGTTCCAAGCATTTAGTGGGAAGAGCTACTCCTTGAAACGTTAGCTGGATTTTGTAG
        ||| |     | ||     |   ||  |||||  | | |||   |   |  | ||     |||| |||    ||  | || |      ||  ||| |||||||| | | ||| || ||  |  |  |||||||||||||   ||  | ||||||||| || || |||||||||||||| |||||||||||||||  ||  ||  
-------ggttgtaggcaattgactccatg-gtccatgctaagtcagcaaagtcactgagtcgtaacattatatgagatgttgctattctgataaattactgt-aacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGC-TTCAGT--
















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|88535455|gb|CI462868.1|CI462868
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88384408|gb|CI551334.1|CI551334
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88322741|gb|CI545447.1|CI545447
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88901899|gb|CI374507.1|CI374507
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88262709|gb|CI366483.1|CI366483
EST:     GAAAGCTGGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAATAAGTACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88458008|gb|CI542190.1|CI542190
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88220249|gb|CI219809.1|CI219809
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88283293|gb|CI404739.1|CI404739
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCCCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|3767687|gb|AU031714.1|AU031714
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGANCCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88553286|gb|CI483386.1|CI483386
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|86428411|gb|CI075092.1|CI075092
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGTCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88506412|gb|CI433918.1|CI433918
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88323941|gb|CI561350.1|CI561350
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88477541|gb|CI414812.1|CI414812
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|11173107|gb|AU164616.1|AU164616
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88515464|gb|CI443118.1|CI443118
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88273589|gb|CI393995.1|CI393995
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88271529|gb|CI387582.1|CI387582
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|86887294|gb|CI313197.1|CI313197
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|86542948|gb|CI183154.1|CI183154
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88971722|gb|CI388966.1|CI388966
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCCCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88549192|gb|CI479056.1|CI479056
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|56158328|gb|C98801.2|C98801
EST:     G-AAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88226010|gb|CI225926.1|CI225926
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88384300|gb|CI551226.1|CI551226
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88437316|gb|CI528675.1|CI528675
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|86498019|gb|CI140652.1|CI140652
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|86868122|gb|CI331873.1|CI331873
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|86430668|gb|CI083091.1|CI083091
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88502106|gb|CI429612.1|CI429612
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
EST: gi|88832890|gb|CI369780.1|CI369780
EST:     GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAG                         GCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA
genomic: GAAAGCTTGTTTTCGGTTCAAGTGCAAACAACAACAAAGAACCGCAAAAGgtattacatt ... ttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatggatatgccgactagttattgattcttttttttttttttttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAAGCATTTAGTGGGAAGAGCTACTCCTTGAAACGTTAGCTGGATTTTGTAG
                      tattgat  putative branch site (score: 3)
                     ttattgattctttttt  CT-rich tract
                  tagttattgattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagcagagttttgattgagtggaatgacatgtttatgctgcctgcattatggatatgccgactagttattgattcttttttttttttttttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGAGCCCAAGTTCCAAGCATTTAGTGGGAAGAGCTACTCCTTGAAACGTTAGCTGGATTTTGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - -ttgattg
- - - - - - - - - - tggaatg
- - - - - - - - - - - - - -acatgtt
- - - - - - - - - - - - - - - - - - - -tgcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tatgccg