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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaaatttccttcacttctgttggacgaaaaacttgaattttcatgttcccttgctagccgcgttagctgatcagaaaattgcgtgattttcag

Basic information

species Oryza sativa
transcript LOC_Os05g28180.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 18
GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaaatttccttcacttctgttggacgaaaaacttgaattttcatgttcccttgct----agccgcgttagctgatcagaaaattgcgtgattttcag
|| ||||||||||| |||||||| | ||||||||||||| | || || |||||||| | ||| ||||| || |||||||||||||| ||||| ||  |||||  ||  | | |  |   | | | |||       || | | |||||  ||    ||  ||    | | |       | |||||                   
GCGCACTGGATTGGTAAGAACTACTTCAAAAGAGGACCTGCTGGAAATGATATTCACAGAACCAATGTACCGCACATCAGGGTTCAATTTAGAGAGATGgtataaa--attctgttctccctttattgtcttggcaagtggtattttggtgaaatctgactcttaaactgttcccctttatcag-------------------
















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|29675538|gb|CB671813.1|CB671813
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|58670237|gb|CK058923.1|CK058923
EST:     TTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: TTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88833424|gb|CI076905.1|CI076905
EST:     AAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: AAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88906221|gb|CI375293.1|CI375293
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTTTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|89198377|gb|CI007437.1|CI007437
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88964769|gb|CI084767.1|CI084767
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTAAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|27548799|gb|CA767547.2|CA767547
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|29638453|gb|CB643462.1|CB643462
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|86481338|gb|CI123971.1|CI123971
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88842057|gb|CI081313.1|CI081313
EST:     TGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: TGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|29637475|gb|CB642484.1|CB642484
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|88841548|gb|CI080804.1|CI080804
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|86536752|gb|CI176958.1|CI176958
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
EST: gi|87022773|gb|CI269709.1|CI269709
EST:     ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG                         ATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT
genomic: ATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCT

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), 52 (downstream exon)
Score: 19

GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTGgtacgaacaa ... tgattttcagATTTGGAGAGATGAGATGCGTCTTGTATACCTAAACAATGTCATCTTACCTGACGAGGTGGACCAGTAACATGTACCTGGTGTATATGGCGCGGTTGCCA




<











<


<