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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctatgtggggttgtcaatcacaactgcagattgcatgatagtggcttgattgggattatttaacttgttttttttttttttggcttcatgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACCTCAAGTCCAGAGATAAAGAATACCCTGTCCATCCCAGACCATTTTGATG

Basic information

species Oryza sativa
transcript LOC_Os09g34100.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G120300_T01 (Zea mays), 3'ss of exon 7
agctatgtggggttgtcaatcacaactgcag-attgcatgatagtggcttgattgggattatt-taacttgttttttttttttttggcttcatgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACCTCAAGTCCAGAGATAAAGAATACCCTGTCCATCCCAGACCATTTTGATG
  | ||      ||        || |||||  | |  |  | || |  ||        ||| | | || |    |  ||  |      |||| ||| || ||||||||||||||||||| || |||||| | |||||||||||  || ||||||| | |||||| || ||||  || |||||| | ||||| ||||| ||||
-tccataatttatttcatgatccatctgcaatacttaactagagagcgtttccaccttttactctgaccttaaatccttaatccaaatttcacgtttgc-agGTGCCAACAACAATTGGAAGGGAGAAGGAATGCAATCCTTTCTTGCGGACCTCCAATCCAGAAATTAAGAGAACACTGTCCGTTCCAGATCATTTCGATG
















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|29646196|gb|CB651203.1|CB651203
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|33653868|gb|CF276482.1|CF276482
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|86260365|gb|CI066238.1|CI066238
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|86518789|gb|CI158995.1|CI158995
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|33692929|gb|CF321168.1|CF321168
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|29640048|gb|CB645057.1|CB645057
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|396941317|gb|HO188526.1|HO188526
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|88263418|gb|CI367192.1|CI367192
EST:     CTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGGGCAATCCTTTTGTGAGGACC
genomic: CTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|8404553|gb|AU091907.1|AU091907
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|29669024|gb|CB665299.1|CB665299
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|86875951|gb|CI325519.1|CI325519
EST:     GCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCAAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: GCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|33680535|gb|CF308774.1|CF308774
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGTAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|86863513|gb|CI345233.1|CI345233
EST:     AGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|86437889|gb|CI119809.1|CI119809
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|29684581|gb|CB680856.1|CB680856
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|33817140|gb|CF334408.1|CF334408
EST:     GCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: GCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|29645268|gb|CB650275.1|CB650275
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|88994083|gb|CI116047.1|CI116047
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACTATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|29645986|gb|CB650993.1|CB650993
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|88248027|gb|CI246645.1|CI246645
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|29656927|gb|CB653202.1|CB653202
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|33680534|gb|CF308773.1|CF308773
EST:     GGAATACGCTGCAANATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGTAGA-AGAAAGCAGTGCAATCCTTTTCTGAGGAC
genomic: GGAATACGCTGCAA-ATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAA-GCAGTGCAATCCTTTTCTGAGGAC
EST: gi|29645569|gb|CB650576.1|CB650576
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|86429896|gb|CI082319.1|CI082319
EST:     AGGTATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|86497845|gb|CI140478.1|CI140478
EST:     GGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCGC-CG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGAC
genomic: GGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACC-CACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGAC
EST: gi|29663513|gb|CB659788.1|CB659788
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|33822569|gb|CF337090.1|CF337090
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|86839638|gb|CI340103.1|CI340103
EST:     ATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: ATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|89168436|gb|CI109640.1|CI109640
EST:     GAGGAATACACCCACG                         GTGCCAACTACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: GAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|30227181|gb|CB965073.1|CB965073
EST:     AATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|29663511|gb|CB659786.1|CB659786
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|88840699|gb|CI080153.1|CI080153
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG                         GTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCC-TTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
EST: gi|58688129|gb|CK076816.1|CK076816
EST:     AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCAGG                         GTG-C--CAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC
genomic: AGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACC

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: 28 (upstream exon), 74 (downstream exon)
Score: 3

AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACGgtattagtgc ... tgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACCTCAAGTCCAGAGATAAAGAATACCCTGTCCATCCCAGACCATTTTGATG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgattgggattatttaacttgttttttttttttttggcttcatgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACCTCAAGTCCAGAGATAAAGAATACCCTGTCCATCCCAGACCATTTTGATG
              atttaac  putative branch site (score: 3)
                        ttttttttttttttgg  putative PPT
           attatttaacttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctatgtggggttgtcaatcacaactgcagattgcatgatagtggcttgattgggattatttaacttgttttttttttttttggcttcatgttcgccagGTGCCAACAACAATTGGGAGAGAGAAGCAGTGCAATCCTTTTCTGAGGACCTCAAGTCCAGAGATAAAGAATACCCTGTCCATCCCAGACCATTTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- ctatgtg
- - - - - - - - - - - -aactgca
- - - - - - - - - - - - - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - - - - -ttgattg