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

ACCGGCCGCTCCGCACGCTCGACCCCACCCAGGACCAGAAGCTCATGTTCGGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcctctctctctccccccacctcaacagagttcttggatcgaaccgctagtggtttggaatggattactttacttattgttactacctacaag...

Basic information

species Oryza sativa
transcript LOC_Os01g33020.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g33020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G010146_T02 (Zea mays), 5'ss of exon 1
ACCGGCCGCTCCGCACGCTCGACCCCACCCAGGACCAGAAGCTCATGTTCGGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactac--gcctctctctctccccccacctcaac-agagttcttggatcgaaccgctagtggtttggaatggattactttacttattgttactacctacaag--
|||| || |||||||||||||||||||||||||| || |||||||||||||| |||||||||||||| ||||||||||||||||||||||| || |||||||||  |   | ||||  ||| |   |||       || | |  |  |  ||  || | |    | ||||   || | ||  |  || | | |||| |    |  
ACCGCCCCCTCCGCACGCTCGACCCCACCCAGGATCACAAGCTCATGTTCGGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtcctacttctcgatcttctagcactcgtgtgagcggttatttactgaggcggtcgctagtcggaa---ataatttcgc--atcgatcctacatcagggta

upper sequence: LOC_Os01g33020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G039373_T01 (Zea mays), 5'ss of exon 1
ACCGGCCGCTCCGCACGCTCGACCCCACCCAGGACCAGAAGCTCATGTTCGGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactac--gcctctctctctccccccacctcaac-agagttcttggatcgaaccgctagtggtttggaat---ggattactttacttattgttactacctacaag
| || ||||||||||||||||| |||||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||| || |||||||||  |   | ||||  ||| |   |||       || | |  |  || ||  ||   ||   | ||||    | | || ||| || || | | || | |     
ATCGCCCGCTCCGCACGCTCGATCCCACCCAGGACCACAAGCTCATGTTCGGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtcctacttctcgatcttctagcactcgtgtgagcgattatctattgagacggccgttagtcggaactcggaaataattt-ctcatcgattctgcat-----

upper sequence: LOC_Os01g33020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S91_249V6.1 (Physcomitrella patens), 5'ss of exon 1
ACCGGCCGCTCCGCACGCTCGACCCCACCCAGGACCAGAAGCTCATGTTCGGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgta-----ctacgcctctctctctccccccacctcaacagagtt--cttggatcgaaccgctagtggtttggaat--ggattactt--tacttattgttactacc----tacaag--------------------------------------------
  || || | |  ||| ||   || |   ||||||||||||||||||||||| ||||| || || |||   || ||||| ||||| || ||||||     ||      || ||| | | | |        |  |    |   ||   |||   |   || ||  |  | |    |   |   |  |  |  || |  || |  ||    ||| ||                                            
GGCGCCCTCACAACACTCTTAGCCACCAGCAGGACCAGAAGCTCATGTTCGGGCTCCTGTTTTCTCTCAAATCTTTCACTGCCAAAATGGATCCCGTTGGgtgggtctcttcgcttattttttattttttatttttttatttttattttgttcccctcccctccttctctaccttctaggccatctcttgtttgtctttgccgccctggtacgaggcctccactatgctgataaatgagtgggtggtggcgatctgcag

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|88832255|gb|CI017489.1|CI017489
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|88988903|gb|CI040635.1|CI040635
EST:     CTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: CTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|58589387|gb|CF987695.1|CF987695
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGGCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|88827220|gb|CI777785.1|CI777785
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTG
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTG
EST: gi|86520090|gb|CI160296.1|CI160296
EST:     CCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCAAGGGTTGCTC
genomic: CCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|87028415|gb|CI263757.1|CI263757
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|88338781|gb|CI660552.1|CI660552
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGGCGGGCCAGGGTTGC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGC
EST: gi|88307587|gb|CI643437.1|CI643437
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGC
EST: gi|88312539|gb|CI585062.1|CI585062
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|88717054|gb|CI740564.1|CI740564
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGG
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGG
EST: gi|88832263|gb|CI017497.1|CI017497
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|66923539|gb|CX110387.1|CX110387
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGG
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGG
EST: gi|88664990|gb|CI706268.1|CI706268
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGG
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGG
EST: gi|58658081|gb|CK046761.1|CK046761
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|9865647|gb|AU101397.1|AU101397
EST:     GGCCTCCTCTTCTCCCTCCG-TCTTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|218485437|gb|FG946454.1|FG946454
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGCTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|88719463|gb|CI742973.1|CI742973
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCAC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCAC
EST: gi|88302386|gb|CI668232.1|CI668232
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|89199179|gb|CI255445.1|CI255445
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|218488359|gb|FG945110.1|FG945110
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|88982282|gb|CI027859.1|CI027859
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|88717143|gb|CI740653.1|CI740653
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCACGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
EST: gi|58599380|gb|CK009908.1|CK009908
EST:     GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCAC                         AGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC
genomic: GGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcc ... cactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCGGCCGCTCCGCACGCTCGACCCCACCCAGGACCAGAAGCTCATGTTCGGCCTCCTCTTCTCCCTCCGCTCCTTCACCGCCAAGATCGATCCCACCACgtactacgcctctctctctccccccacctcaacagagttcttggatcgaaccgctagtggtttggaatggattactttacttattgttactacctacaag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC