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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagaatgatccttagggtgcctaaagagatggcttgatgtgagaatagtaatgtattacttctatgtttttcattgttctgtgtctgatccgatttcagCTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATAAATCTTCTGTCAAAGCGGCTTGAAGAGGGAGCAGAAAAGGGTGAGCTGG

Basic information

species Oryza sativa
transcript LOC_Os04g57540.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G413055_T01 (Zea mays), 3'ss of exon 1
aaagaatgatccttagggtgcctaaagagatggcttgatgtgagaatagtaatgtattacttctatgtttttcattgttctgt--gtctgatccgatttcagCTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATAAATCTTCTGTCAAAGCGGCTTGAAGAGGGAGCAGAAAAGGGTGAGCTGG
      |||   | |   | | |  | |  |||| |    |||||  |  |      | ||   |  ||||| |||||  |||  || || | |  || |||||||| |||||||| ||| | ||||| || ||||| ||||||||||| |||||||| |||||||  || || |||||||||| ||||||||||||  |||
-CTTGCTGAGATTGACAAT-CATGGAAAACTGGCATCTAATGAGATCAACATAAATCTCCTGTCAGTTTTTTAATTGTGTTGTTTGTATGCTTCCTTTCCAGCTTGCTGAGATTGTCAATCAAGGAAAACTGGTGTCTGATGAGATCATCATAAATCTGCTGTCAAGACGCCTGGAAGAGGGAGAAGAAAAGGGTGAATTGG

upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G347841_T01 (Zea mays), 3'ss of exon 1
aaagaatgatccttagggtgcctaaagagatggcttgatgtgagaatagtaatgtattacttctatgtttttcattgttctgt--gtctgatccgatttcagCTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATAAATCTTCTGTCAAAGCGGCTTGAAGAGGGAGCAGAAAAGGGTGAGCTGG
      |||   | |   | | |  | |  |||| |    |||||  |  |      | ||   |  ||||| |||||  |||  || || | |  || |||||||| |||||||| ||| | ||||| || ||||| ||||||||||| |||||||| |||||||  || || |||||||||| ||||||||||||  |||
-CTTGCTGAGATTGACAAT-CATGGAAAACTGGCATCTAATGAGATCAACATAAATCTTCTGTCAGTTTTTTAATTGTGTTGTTTGTATGCTTCCTTTCCAGCTTGCTGAGATTGTCAATCAAGGAAAACTGGTGTCCGATGAGATCATCATAAATCTGCTGTCAAGACGCCTGGAAGAGGGAGAAGAAAAGGGTGAATTGG

upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G150014_T03 (Zea mays), 3'ss of exon 1
aaagaatgatccttagggtgcc-----taaagagatggc--ttgatgtgagaatagtaatgtattacttctatgtttttcattgttctgt--gtctgatccgatttcagCTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATAAATCTTCTGTCAAAGCGGCTTGAAGAGGGAGCAGAAAAGGGTGAGCTGG
         | || ||| || |     |  | |  |||    | ||| || ||   |||    |   |    | ||||| |||||  |||  || || | |  || |||||||| |||||||| ||| ||||||| || ||||| ||||||||||| |||||||| |||||||  || || ||||||||||  |||||||||||  |||
---------tgctgaggttgtcagccatggaaaactggtatctaatgagataaacataaatcttctgtcagtttttttttattgtgttgtctgtatgcttcttttccagCTTGCTGAGATTGTCAATCATGGAAAACTGGTGTCTGATGAGATCATCATAAATCTGCTGTCAAGACGTCTGGAAGAGGGAGAGGAAAAGGGTGAATTGG

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|218504868|gb|FG963478.1|FG963478
EST:     GCGATCTCGTCCGCGACGCCCTCGCCTCCCCGGGCCCCTTCTCCGAGCAG                         CTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATA
genomic: GCGATCTCGTCCGCGACGCCCTCGCCTCCCCGGGCCCCTTCTCCGAGCAGgtgaaacgcc ... ccgatttcagCTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATA
EST: gi|2431503|gb|C73923.1|C73923
EST:     G-GATCTCGTCCGCGACGCCCTCGCCTCCCCGGGCCCCTTCTCCGAGCAG                         CTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATA
genomic: GCGATCTCGTCCGCGACGCCCTCGCCTCCCCGGGCCCCTTCTCCGAGCAGgtgaaacgcc ... ccgatttcagCTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtaatgtattacttctatgtttttcattgttctgtgtctgatccgatttcagCTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATAAATCTTCTGTCAAAGCGGCTTGAAGAGGGAGCAGAAAAGGGTGAGCTGG
                                      gtctgat  putative branch site (score: 4)
     aatgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagaatgatccttagggtgcctaaagagatggcttgatgtgagaatagtaatgtattacttctatgtttttcattgttctgtgtctgatccgatttcagCTTGCGGAGATTGTGAATAATGGAAAGCTAGTGTCGGATGAGATCATAATAAATCTTCTGTCAAAGCGGCTTGAAGAGGGAGCAGAAAAGGGTGAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG