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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcagtttctttatgtaatacaaatgcacttttaaatatacttttatatcaattcttcactctatgactcgtttatgattacttaatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG

Basic information

species Oryza sativa
transcript LOC_Os04g30760.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G099696_T01 (Zea mays), 3'ss of exon 4
gtaagtgcagtttctttatgtaatacaaatgcacttttaaatatacttttatatcaattcttcactctatgactcgtttatgattac-ttaatcta-ccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
|| |||| ||||| ||||    |   |||||  |  ||       |||||| | |||   ||    | ||| ||   | ||   |   |||||  |   ||||||| ||||||||||||||||| |||||||||||||| |||||||
gtgagtgtagtttgtttacaggaaggaaatgttccattt------cttttacaccaacctttattaccatggctttatgattcatgtgttaattgaattagGCTCTAGATAAATGGGGAACAATAGATGTGCTGGTAAATAATGCAG

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G351023_T01 (Zea mays), 3'ss of exon 4
gtaagtgcagtttctttatgtaatacaaatgcacttttaaatatacttttatatcaattcttcactctatgactcgtttatg-attacttaatcta-ccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
|| |||  ||||| ||||   ||   || ||  |  ||    |   ||  | | ||||  ||    | |||  |   | ||  |||  |||||  |   ||||||| |||||||||||||| || |||||||||||||| |||||||
gtgagtctagtttgtttacagaaaggaattgttccatt--tcacttttacacaccaatctttattaccatggttttatgattcatttgttaattgaattagGCTCTAGATAAATGGGGAACGATAGATGTGCTGGTAAATAATGCAG

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G24360.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtgcagtttctttatgtaatacaaatgcacttttaaatatacttttatatcaattcttcactctatgactcgtttatgattacttaatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
                |  || || ||| || ||       |||| |     |||  || | ||   | | | |    | |  ||| ||  |    ||||||||||| ||||||||||| ||||||||  |||| ||||||||||
---------------gtgagtgat-caactgtacaccatcttatattccctaatcc-ttatacatcttttcattttccttttgttattt--ttctgcagGCTCTTGACAAATGGGGAACCATTGATGTTGTGGTTAACAATGCAG

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|14980713|gb|BI305391.1|BI305391
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|23514981|gb|BU673887.1|BU673887
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|30227133|gb|CB965025.1|CB965025
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|30227817|gb|CB965709.1|CB965709
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|23512833|gb|BU672855.1|BU672855
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|30226632|gb|CB964524.1|CB964524
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|30227770|gb|CB965662.1|CB965662
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|30228838|gb|CB966729.1|CB966729
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|23514324|gb|BU673583.1|BU673583
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
EST: gi|23513544|gb|BU673187.1|BU673187
EST:     TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA                         GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
genomic: TCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG

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), 33 (downstream exon)
Score: 20

ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCAgtaagtgcag ... aatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttatatcaattcttcactctatgactcgtttatgattacttaatctaccagGCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG
                                         acttaat  putative branch site (score: 20)
                                tttatgattacttaat  TA-rich tract