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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCTTGCCTTCTGCAAGTTCTTGGTGACTCCATCTACTTTATTGATATTGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgcaattctcgtatgttaaaaaaattgtaatgcagttctcctgcatagcaaaacttttttcttatgatccatcagttccttgtttagcatgtacttacagtaaatgcttgtgtgtgcatggcag

Basic information

species Oryza sativa
transcript LOC_Os11g39020.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g39020.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G105570_T01 (Zea mays), 5'ss of exon 6
GAGGCTTGCCTTCTGCAAGTTCTTGGTGACTCCATCTACTTTATTGATATTGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca--attctcgtatgttaaaaaaattgtaatgcagttctcctgcatagcaaaacttt-tttcttatgatccatcagttccttgtttagcatgtacttacagtaaatgcttgtgtgtgcatggcag
 |||||||| || ||||||||| ||||||||||||||||| || | || ||||||||||| ||||| || |||||||| ||||| ||||||||||||||||| |||  ||   ||||| |    || || |||     |  |         | |  |   | | | | ||| ||      | ||    || | ||||| | | |   | ||  |  || ||  |||||| |||
AAGGCTTGCATTTTGCAAGTTCATGGTGACTCCATCTACTCTACTCATCTTGGATGAACCGACAAACCATCTTGATATCCCATCAAAAGAAATGCTTGAGgtcagagacacggttctcattctatacaataatcagtttttatgatctagccgtccctctattctatctctgatatgggctgaggaaattttctagca-gcagtcctaatagct--ttttgcatgcatgacag

upper sequence: LOC_Os11g39020.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G15200.1 (Glycine max), 5'ss of exon 6
GAGGCTTGCCTTCTGCAAGTTCTTGGTGACTCCATCTACTTTATTGATATTGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgcaattctcgtatgttaaaaaaattgtaatgcagttctcctgcatagcaaaacttttttcttatgatccatcagttccttgtttagcatgtacttacagtaaatgcttgtgtgtgcatggcag
  |||| || || ||||| ||| |||| |  ||||| ||| |  |  | |||||||||||||| |||||| | ||||| || || ||||||||||| |||||| |   || || |    |||        ||   ||  |     | | | |  ||   ||||   | ||         | ||| |     ||                                     
ACGGCTGGCTTTTTGCAAATTCATGGTAAAACCATCAACTCTGCTTGTGTTGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctcacttttgccgtgt-----gcttttccatataaaaaacttac-tgtcac--ctttcagcctactgatttctaattcttctcccag-------------------------------------

upper sequence: LOC_Os11g39020.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G39670.1 (Glycine max), 5'ss of exon 6
GAGGCTTGCCTTCTGCAAGTTCTTGGTGACTCCATCTACTTTATTGATATTGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgcaattctcgtatgttaaaaaaattgtaatgcagttctcctgcatagcaaaacttttttcttatgatccatcagttccttg--tttagcatgtacttacagtaaatgcttgtgtgtgcatggcag
  |||| ||||| ||||| ||| |||| |  ||||| ||| |  |  | |||||||||||||| |||||| | ||||| || || ||||||||||| |||||| |   || || |   || |                  | | | ||  |||  | ||     || || | | |  ||||     ||  ||  |  | | ||  |||                        
ACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTGTTGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctcacttttgtcatat------------------gcttttctatataaaataaaaagcttgttgtcacctttcagcctgctgatttctgattcttctcccag------------------------

upper sequence: LOC_Os11g39020.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G64840.1 (Arabidopsis thaliana), 5'ss of exon 5
GAGGCTTGCCTTCTGCAAGTTCTTGGTGACTCCATCTACTTTATTGATATTGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttag----atgcaattctcgtatgttaaaaaaattgtaatgcagttctcctgcatagcaaaacttttttcttatgatccatcagttccttgtttagcatgtacttacagtaaatgcttgtgtgtgcatggcag
| | ||||| |||||||| ||| ||||||| |||||||||||| |  | ||||| |||||||| |||||| | || ||||| || ||||||||||| ||||||||    | |||  |||  | |||| | ||  ||   || || |  |  |   |  |    | |    ||   |||     | |||  | |||    || |                               
GCGTCTTGCTTTCTGCAAATTCATGGTGACGCCATCTACTTTACTCGTTTTGGACGAACCAACCAATCACTTAGACATTCCTTCAAAAGAAATGCTCGAGgttagtagtaggcatctctaatttgttgagaatctttggatacaatgataataact--ctgttcctggacctggagataggctaattctctttttcaattgaatcag---------------------------

upper sequence: LOC_Os11g39020.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S125_77V6.1 (Physcomitrella patens), 5'ss of exon 8
GAGGCTTGCCTTCTGCAAGTTCTTGGTGACTCCATCTACTTTATTGATATTGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatg----caattctcgtatgttaaaaaaattgtaat-gcagttctcctgcatagcaaaacttttttcttatgatccatcagttcctt---gtttagcatgtacttacagtaaatgcttgtgtgtgcatggcag---------------------
  | || || || ||||||||| ||||||| ||||| ||  |  |||| ||||| ||||| |||||||| ||||||||||||||||| |||||| | ||||| || |     | |  | | |    |   | | |  |  | | |   |  ||  | |       ||| ||  |  | |   |||  |||||     |||||   |   |  | || |  ||  |  | |   |                         
TCGACTAGCATTGTGCAAGTTCATGGTGACGCCATCGACGCTGCTGATTTTGGACGAACCTACAAATCATCTTGATATTCCATCGAAGGAAATGTTAGAGgtgagttaaccacgaaccccatgcaattggacattcttggtagtaaaccatctaaagacttg--ttttcttggttggctgtttcaagtccttcaaaattagctcattaatgtattacactctaata-gagtgcgatcttttaatgcgcttattgggcag

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|29676179|gb|CB672454.1|CB672454
EST:     TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|33798171|gb|CF324944.1|CF324944
EST:     TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|29677239|gb|CB673514.1|CB673514
EST:     TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|29620704|gb|CB625715.1|CB625715
EST:     AGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: AGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|87006701|gb|CI285735.1|CI285735
EST:     GGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|29681743|gb|CB678018.1|CB678018
EST:     ACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: ACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|29677126|gb|CB673401.1|CB673401
EST:     AACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: AACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|29625501|gb|CB630512.1|CB630512
EST:     TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|29676535|gb|CB672810.1|CB672810
EST:     GATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: GATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|29674816|gb|CB671091.1|CB671091
EST:     TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: TGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
EST: gi|29676536|gb|CB672811.1|CB672811
EST:     ACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAG                         GAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG
genomic: ACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGG

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: 75 (upstream exon), 75 (downstream exon)
Score: 123

GAGGCTTGCCTTCTGCAAGTTCTTGGTGACTCCATCTACTTTATTGATATTGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgca ... tgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGGTATTTCGTAAAGCAAATTGTTAACAGAGTTATTGAAGTGAAAGATCAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCTTGCCTTCTGCAAGTTCTTGGTGACTCCATCTACTTTATTGATATTGGATGAACCAACAAATCACCTTGATATTCCATCGAAAGAAATGCTTGAGgttagatgcaattctcgtatgttaaaaaaattgtaatgcagttctcctgcatagcaaaacttttttcttatgatccatcagttccttgtttagcatgtacttacagtaaatgcttgtgtgtgcatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA