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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggatttcttgccttctctttatactatttatttatactgtgtttagtttgggtatactgcatgcactggaatccaacgctttgggtttgatcgacttgtttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG

Basic information

species Oryza sativa
transcript LOC_Os03g47770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 2
gtgggatttcttgccttctctttatactatttatttatactgtgtttagtttgggtatactgcatgcactggaatccaacgctttgggtttgatcgacttgtttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG
                  ||  |||  | |      ||    | ||  ||||| || | || |  |   | |   |      |||  ||    | | |||  |||  || |||| |||||||| |||||||| || |||||||| ||||||||||| ||||| || ||||||||||
-----------------gtcaatatcttctcccccgattgattattgcgtttgcgtgtgcttcgggttttagtgcct----ttttttgtaatgttgtcttcctttgttgcagGTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 1
gtgggatttcttgccttctctttatactatttatttatactgtgtttagtttgggtatactgcatgcactggaatccaacgctttgggtttgatcgacttgtttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG
             |  | |||| |  |    | || |||     |||   |||  | |   |  ||||  ||  |  |  || ||   ||   | |  || ||||| |  |||| |||||||| |||||||| || |||||||| ||||||||||||||||| || ||||||||||
-----------gtcaatatcttcagtccccattttgataaaaattttcaattga-tttttagtgtgcatcgggttttagtgccttcccttatgttgttttattttttt-cagGTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 3
---gtgggatttcttgccttctctttatactatttatttatactgtgtttagtttgggtatactgcatgcactggaatccaacgctttgggtttgatcgacttgtttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG
    ||| || | |||   | |||  |    | ||   |   ||||  ||   ||        ||  |||  | |     || | |||   |||  |  |     | || |  |||| || |||||||||||||| ||  ||||||| ||||||||||||||||||||||| ||| |||
gtcatggaatgttttgatctgtctcgagttgacttgagttctctgttctttacttc------ttgtttgcgtttg----taatgtttttttttttttaaa-----tattgtacagGTGATTTTTCTTCATCCAGCTCCTCTGCATCCTCACATTTACAGCAATGGGCATATTTGTCTAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 3
gtgggatttcttgccttctctttatactatttatttatactgtgtttagtttgggtatactgcatgcactggaatccaacgctttgggtttgatcgacttgtttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG
          |||   | |      |  |  | | || |  |||||         | |  |||| | | ||  ||   |   || |   ||  ||   |  |  ||   |||||  | ||| | |  ||||| ||  ||||||| ||||| |||||||||||||||||||||||||
--------gtttgtgatgttaaagaaacaaatgtgtaaaaagtgttattgaaacttttcttgcacgtattgtgatttta-atttcg---ttattctggtattggttgaatagGTTGTTTTTGTCCCGCCAGCTCCTCTGCATCCTCACATATACAGCAATGGGCATATCTGTTTAG

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|88996042|gb|CI037333.1|CI037333
EST:     AGCATTACCCCATGGAGGCTCCCCAG                         GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
genomic: AGCATTACCCCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
EST: gi|8859712|gb|AU097030.1|AU097030
EST:     ACCAATTGCAGGTGGACTTCCCTGAGCATTACCCCATGGAGGCTCCCCAG                         GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
genomic: ACCAATTGCAGGTGGACTTCCCTGAGCATTACCCCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
EST: gi|568905|gb|D39754.1|D39754
EST:     ACCAATTGCAGGTGGACTTCCCTGAGCATTACCCCATGGAGGCTCCCCAG                         GTCATATTTCTTCATCCAGCGCCAAT
genomic: ACCAATTGCAGGTGGACTTCCCTGAGCATTACCCCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAAT
EST: gi|33813694|gb|CF332734.1|CF332734
EST:     ATTACCCCATGGAGGCTCCCCAG                         GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
genomic: ATTACCCCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
EST: gi|87034301|gb|CI188925.1|CI188925
EST:     ACCCCATGGAGGCTCCCCAG                         GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
genomic: ACCCCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
EST: gi|86432724|gb|CI086335.1|CI086335
EST:     GAGCATTACCCCATGGAGGCTCCCCAG                         GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
genomic: GAGCATTACCCCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
EST: gi|88206195|gb|CI206044.1|CI206044
EST:     CCATGGAGGCTCCCCAG                         GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
genomic: CCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
EST: gi|11565148|gb|AU165784.1|AU165784
EST:     ACCAATTGCAGGTGGACTTCCCTGAGCATTACCCCATGGAGGCTCCCCAG                         GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG
genomic: ACCAATTGCAGGTGGACTTCCCTGAGCATTACCCCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGG

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: 64 (upstream exon), 74 (downstream exon)
Score: 48

GGTCATCGAGGTCGCGGGGGCTGCGGGCACGCTCTATGCCGGAGAGACATACCAATTGCAGGTGGACTTCCCTGAGCATTACCCCATGGAGGCTCCCCAGgtgggatttc ... ttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgcatgcactggaatccaacgctttgggtttgatcgacttgtttttctgtagGTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG
                              gtttgat  putative branch site (score: 48)
                                        cttgtttttct  putative PPT
                                         ttgttttt  TA-rich tract