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

gtgtgtcttttgatttcacagttgtattttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT

Basic information

species Oryza sativa
transcript LOC_Os11g14430.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 4
gtgtgtcttttgatttcacagttgtatt---ttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT------
|||||  || || ||||    |||| ||   ||||||  || | || |||  ||  ||||||  ||  | || || |     ||||||   |||||||||| |||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||||||||||| | ||| | |||||||      
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgc---acaggatcagCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACTTCAAGG

upper sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G103430_T05 (Zea mays), 3'ss of exon 3
gtgtgtcttttgatttcacagttgtatt---ttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT
|||||  || || ||||    |||| ||   ||||||  || | || |||  ||  ||||||  ||  | || || |     ||||||   |||||||||| |||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||||||||||| | ||| | |||||||
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgc---acagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT

upper sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0048g02700.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgtcttttgatt-----tcacagttgtattttgtacgacaaaggtcccaagtttgctaatagagatgtt------ctcttggtc--ctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT
|||    |||  |||     | ||  |     ||  |   | || |     | |  |||| ||      ||       || ||| |    | ||||||   ||  | ||||||||||| ||||| ||    |||||||||||||| ||| | ||||||||||| ||||  ||||||||| ||||     |||| |
gtgcagttttgaattgaaattgactatccaccttattttaagaatgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT

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|29639969|gb|CB644978.1|CB644978
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|218479912|gb|FG956819.1|FG956819
EST:     GTGTTGTCAACATTGAGA-G-TCAAG                         GGTTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: GTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|29664577|gb|CB660852.1|CB660852
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|58609361|gb|CK037394.1|CK037394
EST:     AGATAATCCAGGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|58693279|gb|CK081966.1|CK081966
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|29640012|gb|CB645021.1|CB645021
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|38473107|gb|CF957239.1|CF957239
EST:     GGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: GGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT

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), 73 (downstream exon)
Score: 38

GCTATTCGTTGGTAATGTACCCAAGGGGTTGGGTGAGGAGGAGCTGAGAAAGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT
                        tgctaat  putative branch site (score: 38)
                                      ttctcttg  putative PPT
                           taataga  TA-rich tract