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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacagttcatgaggcagcctttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 2
gttacagttcatgaggcagcctttctataa-attctgttca--------agaaattatat-ttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
                            || | |||| |||        |||| | | |  ||| |||||||||  |  | |||| |||||| | |||||| || |||||||||||||||||||||| | |||| ||||||||||||||||| || |||||||||||||||||||| ||||| ||||| |||||||||||
nnnnnnnnnnnnnnnnnnnnnnnnnnnnaatactctgctcacaggtcgcagaagtgacagattatctgatcatgctcaggcttttctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAACTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 4
-----gttacagttcatgaggcagcctttctataaattct-----gttca-agaaattatat-ttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
       |  | || ||  | | | | || | ||   |       ||||| |||| | | |  |||||||| ||||  ||||||||  |||||| | |||||| || |||||||||||||||||||||| |||||| ||||||||||||||||| || |||||||||||||||||||| ||||| ||||| |||||||||||
gtttgaatcgaatttatctgtctgtccttgtgtactctgctcagagttcacagaagtgagagattacctgaccatgctcttgttttcctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAATTGGGTATCAATGATATTGTTGTGGCTGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 4
----------------------------gttacagttcatgaggcagcctttctataaattctgttcaagaaa-----ttatatttacctg-atcatg-ggcttgtttttatttcctt--tctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
                              || | || ||  |   ||  |||  |   || |   || |  |     | |  | |   || |||||  | |   ||  | | | |    |||||||| || ||||| || |||||||||||||   |||| ||||||||||||||||| || |||||||||||||||||||| ||||| ||||| |||||||||||
gtctgaagctaattcatctatccatgtttgtataattgatctgcttgctgttcattgttttttacacatgtgaagtgttcaggtgtgtgtgtatcatctgaccaattactctctgcacactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 4
gttacagttcatga-ggcagcctttctataaattctgttcaaga---aattatatttacctgatcatgggcttgtttttatttccttt-ctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
  |   ||| || |    | |  ||||||   ||   ||  |     | ||| |  ||    |  | |   ||    || ||    ||  ||||||  ||||| |||| ||||||   |||| ||| ||||  |||||| ||||||| || ||||| |||||||||||||||||||  || || ||| | |||||
-gtgt-gtttataataaaaacaattctatttgtttctttgtatttttatttaaaaatatagaaaaaggatattaaccttgttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAGGCACAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G39870.1 (Glycine max), 3'ss of exon 4
----------gttacagttcatgaggcagcct-ttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
           ||   ||| ||  || ||  | ||| |  | | |   | ||  |  |  ||||   | ||  |||    ||  || |        |||||| || ||| |||||||||   | || | ||| ||  |||||||| ||||||| || ||||| |||||||||||||||||||| || || ||| |||| ||
gtatgctgtttttcttgttgatttggaagggtattccactattcccacttaaatatatgaattt---taat--tggaagggtccttgtc-----attgcagCTACCATGCTTGCAGCACTCACCATACAATTTGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGCACCTAAGTACCTTGCAGA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 4
---------------gttacagttcatgaggcagcct-ttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
               |||   ||| ||  || ||  | ||| |  | | |   | ||  |  |  ||||   | ||     |  |  ||||          |||||| || ||| |||||||||   | || | ||| ||  |||||||| ||||||| || ||||| |||||||||||||| ||||| || || |||||||| ||
gtatgttctttttttgttgttgttgatttggaagggtattccagtattcccacttaaatatatgaattt---taattggaagggtcctttt-------cattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
--------gttacagttcatgaggcagcc-tttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
         ||| |           |    ||||| |  ||| |||| || |||| |||   |   |||  |   |||||| |  ||       ||||||  ||||| |||| ||||||   |||| |||  |||| |||||| ||||||| || ||||| |||||||||||||||||||  || || ||| | |||||
gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaat-ataggaaaaggatattaaacttgttctggtt-----attgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 4
gttacagttcatgaggcagc--ctttctataaattctgttcaagaaattatatttacctgatcatgggcttgtt-tttatttcct--ttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
|| | |  |  ||   ||    |  |||  |  || |   |     |||  ||     |||  |||   || |  ||| |||  |  || | |||||  |||| |||| || ||    || |  || || ||||||||| | ||||| || ||||| |||||||||||||||||| | ||||||||  | || ||
gtgagaactt-tggaacatttgcgctctgcattttttagacttttgatttgatgcttttgacaatgtttttctggtttgtttggtggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTGTGGCGGGTGGTATGGAAAGCATGTCTAATACACCAAAATATTTGGCAGA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 3
----------------gttacagttcatgaggcagcctttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
                ||   |    || |    |  ||   |   ||  | |      |||  |||  |  ||         |  ||||| | | |||  | |||| | ||||||||| |||||||| || | ||||||  |||||||| | ||||| || |||||||||||||| ||||||||||| || |||||| | |   |
gtagattctattatctgtgggaaactataaatttgagttgtcaattatcatatgtggacaatattatcaaagtgtatgacttgtcctttttgtcttcttgatccagCTATAATGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0089g00570.t01 (Vitis vinifera), 3'ss of exon 1
gttacagttcatgaggcagcctttctataaattctgttcaagaaattatattt-acctgatca-tgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTAT--TGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA------
   ||| || |  |  ||||| |     | | ||  ||||| || | |  ||| | |  || | |   ||     | |      || | ||       || |   ||   |      |  |   |  | |  |||||| | ||||| || |||||||||||||| ||||||||||| || |||||| | |  ||      
--cacaattgaataaacagccata----atactcccttcaaaaattgaactttcagcaaatgactaaactaaagatcaggattattttacaattttt-tggtgatagTTTAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 4
--gttacagt-tcatgaggcagcctttctataaattctgttcaagaaattatatttacctg----atcatgggcttgtttttat-ttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
  |  ||  | |||| ||  |     ||| |   |  |   | | || | | | | |  ||    |||||||  || |||| ||  |  |   |||||| |||||| | |||||||||   || |  |||||  ||||||||||||||||  | ||||| |||||||||||||||||||  || |||||| | || ||
gtgccactctatcatcagaaacagcatcttttcctctttccccaaaactgacactaaagtgtaatatcatgg--ttcttttaatgctggtaattgcagCAACAATGCTCGCAGCACAGAGTATCCAGTTGGGTGTCAATGATATTGTTGTGTCTGGTGGTATGGAAAGCATGTCTAATGTGCCTAAATACCTAGCAGA

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|58685561|gb|CK074248.1|CK074248
EST:     CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
genomic: CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
EST: gi|29640957|gb|CB645964.1|CB645964
EST:     CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
genomic: CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
EST: gi|88387760|gb|CI585463.1|CI585463
EST:     CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
genomic: CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
EST: gi|88300828|gb|CI589820.1|CI589820
EST:     ACAGTTGTTTGCAGCCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCAC
genomic: ACAGTTGTTTGCAGC-GCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCAC
EST: gi|58683479|gb|CK072166.1|CK072166
EST:     CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAG                         CGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG
genomic: CACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgttacagttc ... ctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
                  acctgat  putative branch site (score: 4)
                               cttgtttttatttcct  putative PPT
     agaaattatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacagttcatgaggcagcctttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA