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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCCCGCTCCGCGGCGAGTCCTGCGTCGCCGGCTTCCTCCACCAGTTCGCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacgctcctcctcctcgctgcttgccatttgattcgattccccgttgcgcaattgagcttggaaattggggggaattttaggtcccgttcgaat...

Basic information

species Oryza sativa
transcript LOC_Os08g43320.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g43320.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G157384_T01 (Zea mays), 5'ss of exon 1
GGAGCCCGCT--CCGCGGCGAGTCCTGCGTCGCCGGCTTCCTCCACCAGTTCGCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacgctcctcctcctcgctgcttgccatttgattcgattccccgttgcgcaattgagcttggaaattggggggaattttaggtcccgttcgaat---
   || ||    | ||| || || |   |  |||||  |||||| || |||| |||||||||||||||| |||||||||||| ||||||| ||||||||||||||||   ||   |||||   |||   |||| ||||   ||   |  | |        |||     |          ||  ||| |||    ||  |      
--CGCTCGGCGGCGGCGCCGGGTGCGTGGCGGCCGGTCTCCTCCGCCGGTTCTCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcgtcactcct---cgcgaattgcgatttcgctcctgtttctgcccaattgttggatccgatgcgaaattggggtttcaggaagggtctgtgacgg
















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|88578238|gb|CI687158.1|CI687158
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|88326225|gb|CI660038.1|CI660038
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|88585749|gb|CI701489.1|CI701489
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|87024401|gb|CI289931.1|CI289931
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCA
EST: gi|88573253|gb|CI664824.1|CI664824
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|88310401|gb|CI659191.1|CI659191
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|88579260|gb|CI688240.1|CI688240
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|86906974|gb|CI292689.1|CI292689
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAG
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAG
EST: gi|86908498|gb|CI291873.1|CI291873
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|88584923|gb|CI702512.1|CI702512
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|88584460|gb|CI702015.1|CI702015
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|29659845|gb|CB656120.1|CB656120
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|86905027|gb|CI289174.1|CI289174
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAG
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAG
EST: gi|33817180|gb|CF334425.1|CF334425
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|88468817|gb|CI696816.1|CI696816
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|29655821|gb|CB652096.1|CB652096
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
EST: gi|88341472|gb|CI635670.1|CI635670
EST:     GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCAC                         TTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA
genomic: GCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCA

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), 62 (downstream exon)
Score: 12

GGAGCCCGCTCCGCGGCGAGTCCTGCGTCGCCGGCTTCCTCCACCAGTTCGCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacg ... cattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCAAGCATGGCGTCTCATTAGCTGTATCTGGCTACATGCTGGCCTAATCCAC




<











<


<









Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCCCGCTCCGCGGCGAGTCCTGCGTCGCCGGCTTCCTCCACCAGTTCGCCTTCCAGCCGCTCCGGGAGAACCCGCTCCTCGGGCCCTCCTCCGCCACgtacgtaacgctcctcctcctcgctgcttgccatttgattcgattccccgttgcgcaattgagcttggaaattggggggaattttaggtcccgttcgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggggaa