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

ACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAATCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttcagttcatctatgctacctcctgaatgaaccaaactttgtataatttgatcacttcctcctgaatgaagcaaactttgtatagtttgatcac...

Basic information

species Oryza sativa
transcript LOC_Os05g41900.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G073535_T01 (Zea mays), 5'ss of exon 2
ACATAAAGACCAACGAGT-AAAAGCTTGATCTGTCCGGTGCCAACCAA---TCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacg------cttcagttcatctatgctacctcctgaatga-acca-aactttgtataatt--tgatcacttcctcctgaatgaagcaaact-ttgtatagtttgatcac-------------------------------------------------------------------------------
     |||| |||| | | |||||||||||| |  ||||||| || ||   ||||||| ||||||||||||||||||||||||| ||||||||||||||||| |||| |        ||| |||||  |||| |  |  |   | | |       |||  |||||   |     |||||  ||   |||||   | |  || |||| ||||| ||                                                                               
----TAAGAACAACAAATCAAAAGCTTGATCAGCTCGGTGCCTACAAAACCTCAACAACCAAGTTTCATGTCTGATCTCGACGTCCAGCTTCCATCTGCCTTTGgtatggctacttctcaattcatg-atgccatgtttttttttatattgtggttttacataatacatagcatcttccagcttcctgaagagtattactgaatagattgataacatcatacacacgaagttcatcttgaacatgcttattagtgttctgtttgcatctgatggtatggcatcatctttgatag

upper sequence: LOC_Os05g41900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G073535_T03 (Zea mays), 5'ss of exon 3
ACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAA---TCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacg------cttcagttcatctatgctacctcctgaatga-acca-aactttgtataatt--tgatcacttcctcctgaatgaagcaaact-ttgtatagtttgatcac-------------------------------------------------------------------------------
                        |||||| |  ||||||| || ||   ||||||| ||||||||||||||||||||||||| ||||||||||||||||| |||| |        ||| |||||  |||| |  |  |   | | |       |||  |||||   |     |||||  ||   |||||   | |  || |||| ||||| ||                                                                               
------------------------TTGATCAGCTCGGTGCCTACAAAACCTCAACAACCAAGTTTCATGTCTGATCTCGACGTCCAGCTTCCATCTGCCTTTGgtatggctacttctcaattcatg-atgccatgtttttttttatattgtggttttacataatacatagcatcttccagcttcctgaagagtattactgaatagattgataacatcatacacacgaagttcatcttgaacatgcttattagtgttctgtttgcatctgatggtatggcatcatctttgatag
















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|88578112|gb|CI674745.1|CI674745
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88321737|gb|CI672879.1|CI672879
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88345430|gb|CI656088.1|CI656088
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88335109|gb|CI658116.1|CI658116
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88570561|gb|CI661934.1|CI661934
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88742013|gb|CI765521.1|CI765521
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88851628|gb|CI674830.1|CI674830
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88336029|gb|CI645630.1|CI645630
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|5004472|gb|AU069621.1|AU069621
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88762082|gb|CI771638.1|CI771638
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|95100761|gb|CI692473.1|CI692473
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58586098|gb|CF984406.1|CF984406
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCGGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88317352|gb|CI628001.1|CI628001
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88340721|gb|CI657213.1|CI657213
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88308075|gb|CI647902.1|CI647902
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58587137|gb|CF985445.1|CF985445
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88342123|gb|CI636481.1|CI636481
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88571462|gb|CI662835.1|CI662835
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|87017183|gb|CI301219.1|CI301219
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88419668|gb|CI686886.1|CI686886
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|33686145|gb|CF314384.1|CF314384
EST:     ACAAACAATTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88576901|gb|CI673440.1|CI673440
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|55431355|gb|CV728690.1|CV728690
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58591899|gb|CF990207.1|CF990207
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|87017263|gb|CI301299.1|CI301299
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|95101042|gb|CI692770.1|CI692770
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88580466|gb|CI697397.1|CI697397
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAATCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttcagttcatctatgctacctcctgaatgaaccaaactttgtataatttgatcacttcctcctgaatgaagcaaactttgtatagtttgatcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT