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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctgtgaatgtgcttctggcacctaatctcatcacatctttcttaagtaaaaacactgttgtgactttgacttaccattattatgctgttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTGTGTGCCTTTCAACAGTATGGCCTCGGTAGGTGTGGTGCGTTCTTCCTTG

Basic information

species Oryza sativa
transcript LOC_Os05g04340.1
intron # 1
splice site 3'
intron type U2

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|88736332|gb|CI759840.1|CI759840
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88308962|gb|CI654245.1|CI654245
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|29628929|gb|CB633940.1|CB633940
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTCGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTT
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGT-GGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTT
EST: gi|88586203|gb|CI703893.1|CI703893
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88400318|gb|CI591008.1|CI591008
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88688717|gb|CI732293.1|CI732293
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88350886|gb|CI619144.1|CI619144
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88298568|gb|CI563563.1|CI563563
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88423830|gb|CI609861.1|CI609861
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|86883938|gb|CI309910.1|CI309910
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|86901784|gb|CI310546.1|CI310546
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88350866|gb|CI619124.1|CI619124
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88389101|gb|CI595335.1|CI595335
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCCCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|86849890|gb|CI301753.1|CI301753
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|86850234|gb|CI305473.1|CI305473
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|58601571|gb|CK012099.1|CK012099
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|58663289|gb|CK051975.1|CK051975
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|33658344|gb|CF280957.1|CF280957
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|86832300|gb|CI307516.1|CI307516
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|29630931|gb|CB635940.1|CB635940
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|58603162|gb|CK013690.1|CK013690
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|86902464|gb|CI304283.1|CI304283
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|29626488|gb|CB631499.1|CB631499
EST:     GCCCCGCTCCGTCCCCTCTACGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88354859|gb|CI614137.1|CI614137
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|29629558|gb|CB634567.1|CB634567
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|25798115|gb|CA754076.1|CA754076
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|58598716|gb|CK009244.1|CK009244
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88342816|gb|CI640149.1|CI640149
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88412181|gb|CI573457.1|CI573457
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
EST: gi|88395838|gb|CI593040.1|CI593040
EST:     GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTG                         GTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG
genomic: GCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTG

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: 72 (upstream exon), 75 (downstream exon)
Score: 44

AGCCAGCGAGGGAGGTGGGGCAATCCAGCGAGCGCCAGATCGTGCCGCCAGCCCCGCTCCGTCCTCTCTCCGGCGACCCTCCGCCCCGCCTGATCCCGTGgtaaatccct ... ttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTGTGTGCCTTTCAACAGTATGGCCTCGGTAGGTGTGGTGCGTTCTTCCTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtaaaaacactgttgtgactttgacttaccattattatgctgttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTGTGTGCCTTTCAACAGTATGGCCTCGGTAGGTGTGGTGCGTTCTTCCTTG
                         gacttac  putative branch site (score: 44)
                                 attattat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctgtgaatgtgcttctggcacctaatctcatcacatctttcttaagtaaaaacactgttgtgactttgacttaccattattatgctgttgtttgcagGTGGATCAACTACAACTCATCTTTAGGAAAGCCTCTTGAACATTAGCCTTGTGTGCCTTTCAACAGTATGGCCTCGGTAGGTGTGGTGCGTTCTTCCTTG

- - -gtgaatg
- - - - - - tgcttct
- - - - - - - - - - gcaccta
- - - - - - - - - - - - - - - - - - - - - - - - - aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgctg