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

AAATGTCATTGAGAAGTGCTTAGCCTTTGGGAATCCTGTAGAACGACAGATTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgcattcttaaaacttatacaaaccaaatttggcttaagatttgtccagctacaagtttgctaaatcttgtaagatggaaagctgattttagagacctgatggaagttaactgcgctgcacctgttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g01910.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01910.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G042623_T02 (Zea mays), 5'ss of exon 8
AAATGTCATTGAGAAGTGCTTAGCCTTTGGGAATCCTGTAGAACGACAGATTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgc--attcttaaaacttatacaaaccaaatttggcttaagatttgtccagctacaagtttgctaaatcttgtaagatggaaagctgattttagagacctgatggaagttaactgcgctgcacctgttgcag---
||||||||| ||||||||||||| |||||| |||||||||||||| ||| || ||||  |||| ||||||||||||||||  || || ||||  |||||||| ||   ||  || |||||| |    | |   ||||   ||   ||| |  |   ||||||   |  |||  | |          | | |      ||  ||||     |||   |||  ||   |||||||     
AAATGTCATCGAGAAGTGCTTAGTCTTTGGAAATCCTGTAGAACGTCAGGTTCTGATTGGTGAGATGCTTGGATCCACTAGCGAAAGCGAACCTCTTGAGgtatggtgatgtttgaaacttttctttatcttctttgaagtagtttttatttaagcacaagtg-accgaatgcttt----------gttcaccacttagtactgacatgggtt---tgcattg--tctgttgcgatag

upper sequence: LOC_Os05g01910.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G012964_T01 (Zea mays), 5'ss of exon 9
AAATGTCATTGAGAAGTGCTTAGCCTTTGGGAATCCTGTAGAACGACAGATTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgc----------attcttaaaacttatacaaaccaaatttggcttaag----atttgtccagctacaa-gtttgctaaatcttgtaagatggaaagctgattt---tagagacct-----gatggaa-gttaactgcgctgcacctgttgcag
 ||||||||||||||||||||||||||||| |||||||||||||| ||| || ||||| |||| ||||||||||||||||  || || ||||  |||||||| |||           |  ||  |  || |   ||  |  |||   |||||    | |   | |  | |   |||| | |     |    |       ||| ||||   | |||| ||     |||   |  |    |||| ||    ||    ||
TAATGTCATTGAGAAGTGCTTAGCCTTTGGAAATCCTGTAGAACGTCAGGTTCTGATCGGTGAGATGCTTGGATCCACTAGCGAAAGCGAACCTCTTGAGgtatgctgatgctttggtctttttattttcttttaagaatgttttatttaagcagaactgaccaaaatgctttgtttaccactcaataactggctagtggctaatttgtcttgagatctttactgataagatatgggttgcgttgtggttgcgctag
















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|66913247|gb|CX100095.1|CX100095
EST:     TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAG                         GTAATGATGAAAGATCAGTTTGCAAACTATGTGGTGCAGAAGGTGCTAGAG
genomic: TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgcattc ... cctgttgcagGTAATGATGAAAGATCAGTTTGCAAACTATGTGGTGCAGAAGGTGCTAGAG
EST: gi|33796513|gb|CF324123.1|CF324123
EST:     TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAG                         GTAATGATGAAAGATCAGTTTGCAA-CTATGTGG
genomic: TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgcattc ... cctgttgcagGTAATGATGAAAGATCAGTTTGCAAACTATGTGG
EST: gi|27548535|gb|CA766537.2|CA766537
EST:     TTTTGATCGGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAG                         GTAATGATGAAAGATCAGTTTGCAAACTATGTGGTGCAGAAGGTGCTAGAG
genomic: TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgcattc ... cctgttgcagGTAATGATGAAAGATCAGTTTGCAAACTATGTGGTGCAGAAGGTGCTAGAG
EST: gi|27577450|gb|CB000145.1|CB000145
EST:     TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAG                         GTAATGATGAAAGATCAG
genomic: TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgcattc ... cctgttgcagGTAATGATGAAAGATCAG
EST: gi|58662202|gb|CK050882.1|CK050882
EST:     TTTTGATCGGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAG                         GTAATGATGAAAGATCA
genomic: TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgcattc ... cctgttgcagGTAATGATGAAAGATCA
EST: gi|58681162|gb|CK069849.1|CK069849
EST:     TTTTGATCGGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAG                         GTAATGATGAAAGATCAGTTTGCAAACTATGTGGTGCAGAAGGTGCTAGAG
genomic: TTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgcattc ... cctgttgcagGTAATGATGAAAGATCAGTTTGCAAACTATGTGGTGCAGAAGGTGCTAGAG

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: 48 (upstream exon), 69 (downstream exon)
Score: 7

AAATGTCATTGAGAAGTGCTTAGCCTTTGGGAATCCTGTAGAACGACAGATTTTGATCAGTGAAATGCTTGGATCCACTAATGAGAGTGAACACCTTGAGgtttgcattc ... cctgttgcagGTAATGATGAAAGATCAGTTTGCAAACTATGTGGTGCAGAAGGTGCTAGAGACTTGTGATGATCAGCAGAGGGAGGCGATCCTTACAAGGATAAAAGCAC




<











<


<