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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCATCTTGTTCCACCAGAGACTCCTCGGTCAATCTTTGTCTACTTCCGTGGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgtatgcacctaattaaattatgcagctgaaaagctgtaggtcttaatcaatcattgattagaaagtcttgatacacctaccattaggttctatattgtgt...

Basic information

species Oryza sativa
transcript LOC_Os10g10080.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g10080.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G059845_T01 (Zea mays), 5'ss of exon 3
CTCATCTTGTTCCACCAGAGACTCCTCGGTCAATCTTTGTCTACTTCCGTGGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgta------tgcacctaat-taaattatgcagctgaaaagctgtaggtc--ttaatca--atcattgattagaaagtcttgatacacctaccattaggttctatattgtgt-----------------------------
||||| | || || |||||||| |||||||| ||||| ||||||||||| ||  ||||||| || ||  |||| || || |||||||||||||||||||||||      |||  | |   | || ||     |  |  ||   |  ||   | |||||  |||| ||||||| |||||||||  ||||| |  |  | | |  |   || |                             
CTCATATCGTCCCGCCAGAGACGCCTCGGTCGATCTTCGTCTACTTCCGCGGCCTGTTCTACGACACCGCGAACGACCCCGAGGGTGGTTACTATGCAAGgtaccgtagtgctacgagcctgaactacctgacaaaggagtccttagtggatgaatcatcatcactgattagcaagtcttgacgcacctgcgctgcgctgccgtgc-gtataactaactgtatacgacgcaacaatgcag

upper sequence: LOC_Os10g10080.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 5'ss of exon 3
CTCATCTTGTTCCACCAGAGACTCCTCGGTCAATCTTTGTCTACTTCCGTGGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgtatgcacc-taattaaattatgcagctgaaaagctgt--aggtcttaatcaatcattgattagaaagtcttgatacacctaccattaggttctatattgtgt-
| ||  |  | || ||||| |||||| |||| ||||||||||||||||| || ||||||||||||      ||||| || || |||||||| |||||||||||| |  |  ||||    ||||  |       | |||  ||   |  |  | | ||  || | | | | || || ||  ||  | |   ||| ||        
CCCACTTGATCCCGCCAGACACTCCTAGGTCTATCTTTGTCTACTTCCGAGGATTGTTCTATGATGTAGGAAATGACCCAGAAGGTGGTTATTATGCAAGgtattcctcacaatttttatatgttgacattggggtgtttagacatcga--agtgat--atgaaatatttttaatgcatgtataaatcctttcaatgggagaga

upper sequence: LOC_Os10g10080.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 5'ss of exon 3
CTCATCTTGTTCCACCAGAGACTCCTCGGTCAATCTTTGTCTACTTCCGTGGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgtatgcacctaattaaattatgcagctgaaaagctgtaggtcttaatcaatcattgattagaaagtcttgatac-acctaccattaggttctata--ttgtgt-
| || ||  |||| | ||| || |||||||| ||||| || ||||||||||||||||| ||||||      ||||| ||||| ||||||||||||||||||||||    | | |   || |    |       || |   ||||| |  |  ||||  | ||||   ||||||| |    | |||   |  ||    ||  || 
CCCACCTAATTCCCCAAGAAACCCCTCGGTCCATCTTCGTTTACTTCCGTGGTTTGTTTTATGATGTGAATAATGACCCTGAAGGTGGTTACTATGCAAGgtatgtgggttagtgttttttttttccttttt-cttttcctctta-ttgagaattgcattgaaa--tttgataccatgggcaattcaataataggggttaggtt

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|8859262|gb|AU096580.1|AU096580
EST:     GGTTTGTTCTATGATACTTCGAATGATC-TGAGGGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCGGTGTGGGAAGAACTTTCAAGAACAANCCGATGTTC
genomic: GGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgtatgcacct ... tgcaatgcagGGGCGCCCGTGCATCGGTGTGGGA-GAACTT-CAAGAACAACCCGATGTTC
EST: gi|8857145|gb|AU094463.1|AU094463
EST:     GGNTTGGTCTATGATACTTCGAATGATCCTGAGGGTGGNTACTATGCAAG                         GGGCCGCCCGTGCATCGGTGTGGGGAGAACTTCAAGA
genomic: GGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgtatgcacct ... tgcaatgcagGGGC-GCCCGTGCATCGGTGTGGG-AGAACTTCAAGA
EST: gi|58656039|gb|CK044719.1|CK044719
EST:     GGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCGGTGTGGGAGAACTTCAAGAA
genomic: GGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgtatgcacct ... tgcaatgcagGGGCGCCCGTGCATCGGTGTGGGAGAACTTCAAGAA
EST: gi|86502920|gb|CI145553.1|CI145553
EST:     GGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAACCCGATGTTCGA
genomic: GGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgtatgcacct ... tgcaatgcagGGGCGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAACCCGATGTTCGA

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: 73 (upstream exon), 43 (downstream exon)
Score: 8

CTCATCTTGTTCCACCAGAGACTCCTCGGTCAATCTTTGTCTACTTCCGTGGTTTGTTCTATGATACTTCGAATGATCCTGAGGGTGGTTACTATGCAAGgtatgcacct ... tgcaatgcagGGGCGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAACCCGATGTTCGACATCTCTACGGACCACCCCCAAACCTACTACGAGGACATGCAGCGTGCA




<











<


<