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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttttgcatagtacagtttcatgaaaaaaaaaaagggactattagctcaatatagctcaaaccagtcttatg...

Basic information

species Oryza sativa
transcript LOC_Os02g42540.1
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttttgcatagtaca-gtttcatgaaaaaa-------aaaaagggactattagctcaat--atagctcaaaccagtcttatg----------------------------------------------------------------------------------
||| |||||||| || ||||| ||||| |||||||||||||| ||||| |||||||| |||||||| | |||||||||||| ||||||||||||||||||||||||| |  |  |  |||     | || ||| | |  || |   || |||| |          || | ||  |  ||||||        | ||     ||   |||                                                                                    
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttt-tgcatagtacagtttcatgaaaaaaaaa-aagggactattagctcaatatagctcaaaccagtcttatg
|||||||||| |||| || || ||||| ||||||||||| ||||| || ||||| || || || || || ||||| || || ||||||||||| ||||||||||||| || |  |  |     |  ||     | |||  | |    || ||     |     |  || | |||  ||  ||   ||  ||  |   |  | 
CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgtttcttcatcttgggttgattttgactgatttttatgtcc-tactactacaattaccttgct-

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA16G33570.2 (Glycine max), 5'ss of exon 4
CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttt-tgcatagtacagt-ttcatgaaaaaaaaaaaggg-actattagctcaatatagctcaaaccagtcttatg
|||||||||| |||| || || || || ||||||||||| ||||| || |||||||| || || || || ||||| || || ||||||||||| ||||||||||||| || |  |  |     |  ||     | |||  |    | |||||         |   |  |||  |   |   |    ||   || ||| |    
CAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgttttcttcttcatcttgggttgatttgatactgatttttatgtcctactactacaagtatc---

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 5'ss of exon 4
CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttt-tgcatagtacagtttc-atgaaaaaaaaaaagggactattagctcaatatagctcaaaccagtcttatg-----------
            ||| || || || || || ||||| |||||||| || ||||| || ||| | ||||| || ||||||||||| |||||||| ||||||||||||| |  | |   |      ||     | || | | ||  ||  |  ||  |        | ||    | |     |   |  ||  | | | ||||            
------------ACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGCATTTAAGATATCCTTTCGTgtgcctttagatttgcaactgtgtacattagggtggctgtgtcattggggttgagatagctcgtaatgttctgg-catgcaaattttattgcaaaaaaaag

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
-------CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttttgcatagtacagtttcatgaaaaaaaaaaagggactattagctcaatatagctcaaaccagtcttatg
        ||||||||||| || ||| ||||||| ||||||||||||||||| || || |||||  | |  || || |||||||| || || || || |||||||| |||||||  | |   | | ||   |||| |||| | ||   ||||   |  | |  ||||  ||    |||| || || ||  |  ||   |   |   |
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatcct--tatgacatttatttattatatttttc-ta--tcagtgctacaatatcaaaattgg----attatctaaaaatgtcagaagtgatggtagag

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|88331773|gb|CI640804.1|CI640804
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88331772|gb|CI640803.1|CI640803
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88381604|gb|CI682270.1|CI682270
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88330892|gb|CI638300.1|CI638300
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88571094|gb|CI662467.1|CI662467
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88453631|gb|CI682502.1|CI682502
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88324974|gb|CI644986.1|CI644986
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88576151|gb|CI670296.1|CI670296
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCT
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCT
EST: gi|27547521|gb|CA765797.2|CA765797
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88501795|gb|CI695478.1|CI695478
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCCA-CAATTTTAGCTGATTCTACACCTGCTGTTCCTGNGGCTCTTCG
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGC-AGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCG
EST: gi|88341833|gb|CI642977.1|CI642977
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|33810840|gb|CF331311.1|CF331311
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGTTCTTCGA
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGA
EST: gi|88320199|gb|CI672378.1|CI672378
EST:     CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCG
genomic: CAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCG

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: 47 (upstream exon), 58 (downstream exon)
Score: 7

CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctctt ... ctgacatcacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTTCCTGCGGCTCTTCGAGTCGAGCCTAAACCTAAAAGCGATATCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttttgcatagtacagtttcatgaaaaaaaaaaagggactattagctcaatatagctcaaaccagtcttatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa