Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGAGGCAATGGTAGATCAAGTATTAGCTGATAATCCAAAGCAACTTGAGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctattctgatttctctgttccccatggtagcgtttgtcttacatcaacagtttaatcaaattatttcaattgtttccag

Basic information

species Oryza sativa
transcript LOC_Os11g34210.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g34210.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G091560_T01 (Zea mays), 5'ss of exon 7
AATTGAGGCAATGGTAGATCAAGTATTAGCTGATAATCCAAAGCAACTTGAGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctattc-tgattt-ctctgttccccatggtagcgtttgtcttacatcaacagtttaatcaaatt-atttcaattgtttccag
||||||||||||||||||| ||||| | ||||||||||||||||||||||||||||| ||  | || ||||||||  | |||||||||||||||||||||||||||| |||  ||| |  | |||||   |     |||   |    |  || | ||||   |||| |||  ||||||||| ||  ||
AATTGAGGCAATGGTAGATAAAGTAATTGCTGATAATCCAAAGCAACTTGAGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaattgatgactagcactgtttgtcccttcagc---taggatgtattatcagt--gatcatatttgtttcaattgattatag
















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|86882758|gb|CI327383.1|CI327383
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|88901789|gb|CI374397.1|CI374397
EST:     GCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAAT
genomic: GCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTG-CTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAAT
EST: gi|86845186|gb|CI340316.1|CI340316
EST:     ACCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|29616532|gb|CB621544.1|CB621544
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|86862767|gb|CI331650.1|CI331650
EST:     GCACTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAAT
genomic: GCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCT-GGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAAT
EST: gi|4714211|gb|AU058178.1|AU058178
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|3760962|gb|C98216.1|C98216
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|89175846|gb|CI042867.1|CI042867
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|88275762|gb|CI396366.1|CI396366
EST:     AGCAGTATCGGTCC-GGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|86883589|gb|CI338107.1|CI338107
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|89181776|gb|CI113282.1|CI113282
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTTGTTGAACGAA-T
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTT-GTTGAACAAAAT
EST: gi|86864344|gb|CI334102.1|CI334102
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|2442947|gb|C74718.1|C74718
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|86493642|gb|CI136275.1|CI136275
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|5607521|gb|AU076170.1|AU076170
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|88470090|gb|CI407361.1|CI407361
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|88476131|gb|CI413402.1|CI413402
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|86600803|gb|CI356560.1|CI356560
EST:     ACCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAAAT
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAA-T
EST: gi|88252153|gb|CI350581.1|CI350581
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|86839311|gb|CI331559.1|CI331559
EST:     AGCACTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|86498082|gb|CI140715.1|CI140715
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|88291582|gb|CI537368.1|CI537368
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|89169673|gb|CI110032.1|CI110032
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|86433685|gb|CI094028.1|CI094028
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|29646032|gb|CB651039.1|CB651039
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|89176251|gb|CI043272.1|CI043272
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|88843573|gb|CI372473.1|CI372473
EST:     GCAGTATCGGTCCGGGAAAACTAAATTGCAAGGANNNNNNNGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: GCAGTATCGGTCCGGGAAAACTAAATTGCAAGGA-TTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|29641132|gb|CB646139.1|CB646139
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|88266019|gb|CI376921.1|CI376921
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|86834558|gb|CI344489.1|CI344489
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC
EST: gi|88282718|gb|CI404114.1|CI404114
EST:     AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTNTTGGACAAAATC
genomic: AGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 55 (downstream exon)
Score: 8

AATTGAGGCAATGGTAGATCAAGTATTAGCTGATAATCCAAAGCAACTTGAGCAGTATCGGTCCGGGAAAACTAAATTGCAAGGATTTTTTGCTGGCCAGgtttgtctat ... ttgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATCCTCGGGGAGAAATTGAAGGCCAATAGTTGAGGGGGTTTGTCGACAAACG




<











<


<