Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatcttgagctttttatcactttcttgtcttctttctcttgatgaattactcatgctcatccatggcaacgatggacgacgatacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATATGTGCGTTGGACTTCCGCATGGATGAGTGGGGAGTGGACGTGGCGCTGAC

Basic information

species Oryza sativa
transcript LOC_Os08g39300.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g39300.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G13360.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaacatcttgagctttttatcactttcttgtcttctttctcttgatgaattactcatgctcatccatggcaacgatggacgacgatacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATATGTGCGTTGGACTTCCGCATGGATGAGTGGGGAGTGGACGTGGCGCTGAC
      || | |  |  | |  | |    ||| ||  || |     ||  ||     |  | |  |      ||  | |       |||   ||||  |  ||| ||| |||||  | || || |||||||| || || || || || ||| | || ||||| ||||||||||||||||||||||||||  ||||
-----gtcattaattcctcacaaataatctgtttttctttt----gtgttttctctgttttaaatctcacttacattaggg---tttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCTGCGCGCTTGATTTCCGAATGGATGAGTGGGGAGTGGACGTGGCCTTGAC

upper sequence: LOC_Os08g39300.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0009g03740.t01 (Vitis vinifera), 3'ss of exon 2
-------------------gtaacatcttgagctttttatcactttcttgtcttctttctcttgatga--attactca-tgctcatccatggcaacgatggacg-acgatacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATATGTGCGTTGGACTTCCGCATGGATGAGTGGGGAGTGGACGTGGCGCTGAC
                   |  ||||||| | ||       |  |||   |     |||| |   |    | || |   | |||||   |  |     |    | |    |    ||||  || || | || || || ||  | || || || ||||||||||| ||||||||  | || ||||| |||||||| ||||||||||| |||||| | ||
gtaagaattcattttctaggccacatcttcatctgcaaggaaacttcacattaggattctgtcattttccactattgggttctcatttttaacgttcttttttgtattgaaatatcagATGAGTACCGTCATCCAGCACTCTTTCTTGTTGATGGGGTGTCATCCATATGTGCCCTTGATTTCCGTATGGATGAATGGGGAGTGGATGTGGCGTTAAC
















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|88367219|gb|CI563983.1|CI563983
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAA-TCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCAT
EST: gi|33666875|gb|CF297842.1|CF297842
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|58608520|gb|CK036553.1|CK036553
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29657961|gb|CB654236.1|CB654236
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|33801638|gb|CF326691.1|CF326691
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|33797630|gb|CF324674.1|CF324674
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29660238|gb|CB656513.1|CB656513
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29671057|gb|CB667332.1|CB667332
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29644601|gb|CB649608.1|CB649608
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29688813|gb|CB685088.1|CB685088
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29615925|gb|CB620937.1|CB620937
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29638362|gb|CB643371.1|CB643371
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|58607598|gb|CK035631.1|CK035631
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29675972|gb|CB672247.1|CB672247
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29678036|gb|CB674311.1|CB674311
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|38471361|gb|CF955492.1|CF955492
EST:     GACCGGCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTAC
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTAC
EST: gi|29638669|gb|CB643678.1|CB643678
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29678170|gb|CB674445.1|CB674445
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29643551|gb|CB648558.1|CB648558
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGAGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29679264|gb|CB675539.1|CB675539
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|38468869|gb|CF953000.1|CF953000
EST:     ACCTGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGTGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATA
genomic: ACC-GCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAG-GCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATA
EST: gi|29668635|gb|CB664910.1|CB664910
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|29664278|gb|CB660553.1|CB660553
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCAACCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT
EST: gi|86894091|gb|CI306055.1|CI306055
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGG
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGG
EST: gi|44670231|gb|CR283665.1|CR283665
EST:     GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCG                         ACAAGCACAGGCACCCGGCGCTACTACAGGTGGACGGGGTGTCATCGATGT
genomic: GACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATAT

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: 49 (upstream exon), 75 (downstream exon)
Score: 3

CGCCAGGACCCCTCCCACTCCATCAAGGCCATCTGCATCGTCCACAACGAGACCGCCACTGGAGTCACCAACGACCTTTCCGCCGTCCGCAAAATCCTCGgtaacatctt ... atacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATATGTGCGTTGGACTTCCGCATGGATGAGTGGGGAGTGGACGTGGCGCTGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatgaattactcatgctcatccatggcaacgatggacgacgatacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATATGTGCGTTGGACTTCCGCATGGATGAGTGGGGAGTGGACGTGGCGCTGAC
 tcttgat  putative branch site (score: 3)
     atgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatcttgagctttttatcactttcttgtcttctttctcttgatgaattactcatgctcatccatggcaacgatggacgacgatacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATATGTGCGTTGGACTTCCGCATGGATGAGTGGGGAGTGGACGTGGCGCTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA