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

gtaacactcgcaaccattatttacccttttgtcttgatatccttggaactttcatattatcaaatccaacttaaaatggaacccatgcatgaccttcttgatatgttcatatataatggttattttagttagcagctcacagattgatttttttcattatcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG

Basic information

species Oryza sativa
transcript LOC_Os01g47262.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47262.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA01G03710.1 (Glycine max), 3'ss of exon 7
gtaacactcgcaaccattatttacccttttgtcttgatatccttggaactttcatattatcaaatccaacttaaaatggaacccatgcatgaccttcttgatatgttcatatataatggttattttagttagcagctcacagattgatttttttcattatcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG
                                                       || |  | | ||||  | |  |  ||  | |  ||      ||  |||     | | | |||       |   ||  |  |||  |   |  | || |  || || ||    ||||||| ||||| ||||  |||||| | |||||  | ||||||||||||||||| |||||||||
------------------------------------------------------gatcactatagccaaaattacttttaaaacctaaat------ctctata-----aaagacaatatcctcctggtttgacttctctaacccttctcttctaaataatttt----agACACATCCTTCTCAAAGTTGTTTCATGTCATCGGTGGATCTGCACACTCAATATTCCTACCAG
















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|44677600|gb|CR291034.1|CR291034
EST:     TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACAT                         ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
genomic: TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACATgtaacactcg ... tcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
EST: gi|218493474|gb|FG952533.1|FG952533
EST:     TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACAT                         ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
genomic: TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACATgtaacactcg ... tcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
EST: gi|33658750|gb|CF281363.1|CF281363
EST:     TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACAT                         ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
genomic: TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACATgtaacactcg ... tcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
EST: gi|29670555|gb|CB666830.1|CB666830
EST:     TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACAT                         ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
genomic: TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACATgtaacactcg ... tcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
EST: gi|88226876|gb|CI224644.1|CI224644
EST:     TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACAT                         ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
genomic: TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACATgtaacactcg ... tcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA
EST: gi|86496637|gb|CI139270.1|CI139270
EST:     TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACAT                         ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTTAA
genomic: TACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACATgtaacactcg ... tcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAA

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: 75 (upstream exon), 63 (downstream exon)
Score: 110

TGCCAGGCTGTCAGTGAGGAGGAGATACATGCTATTTTATCGGAGCAATCACTTTACCCTGCAGGGTGGATACATgtaacactcg ... tcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggttattttagttagcagctcacagattgatttttttcattatcttttccagACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG
                                 tttttttcattatctt  CT-rich tract
                            attgatttttttcatt  TA-rich tract