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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGTATTCCTGAACATCGCAAAGCAGGCAGAACTGGAGAGCTCTACTGCTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttccttagtacccctaagaacaatgctgcaatattggacatgaaaaggataatctcactgctatgtagagaacttctgtacagcagcaacagtac...

Basic information

species Oryza sativa
transcript LOC_Os08g30740.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g30740.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G142249_T01 (Zea mays), 5'ss of exon 15
AGAAGTATTCCTGAACATCGCAAAGCAGGCAGAACTGGAGAGCTCTACTGCTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttccttagtacccctaagaacaatgctgcaatattggacatgaaaaggataatctcactgctatgtagaga-acttctgtacagcagcaacagtac-----------------------------------------------------------------------------------------
||| || ||||||||||| |||||||||||||| ||||||| ||||||||||||||| |||||||| ||||| ||||| ||||||||  || | |||||||| ||| | | |||| |||||| || ||      | |  |   ||| |   |   ||  |  |||  ||| ||| | |  ||    || |   |  |||                                                                                           
AGAGGTGTTCCTGAACATTGCAAAGCAGGCAGAGCTGGAGACCTCTACTGCTGAAGGTACCCTGGTGACTCTCAACCTGTCATCAGGAACAACAATTCAGgtgtgtac-tcagtaaccctaacaataacaacatacttctaaccataattggaggaaaatatctgaaatgcagaaatatctcccatcaactagactagtttgcttatctggttgtttagcaaaggaaaaaaacgctagggatacatttagaagtcttctggtctttgattgtgtctctttgacaattcag
















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|88249764|gb|CI249613.1|CI249613
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|88969369|gb|CI382911.1|CI382911
EST:     ACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: ACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|87041608|gb|CI196230.1|CI196230
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|86478797|gb|CI121430.1|CI121430
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|88236684|gb|CI235886.1|CI235886
EST:     CTGAAGGCACTCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|89181256|gb|CI112762.1|CI112762
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCTAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|29640977|gb|CB645984.1|CB645984
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|86500706|gb|CI143339.1|CI143339
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|58608654|gb|CK036687.1|CK036687
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|33688321|gb|CF316560.1|CF316560
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|86513227|gb|CI155860.1|CI155860
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|87041903|gb|CI196525.1|CI196525
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|8527411|gb|AU092226.1|AU092226
EST:     TGAAGGCACCCTGGTTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGANTCGGAGGAT
genomic: TGAAGGCACCCTGG-TTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|87037618|gb|CI192240.1|CI192240
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|88251613|gb|CI350041.1|CI350041
EST:     CTGAAGCCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|88234185|gb|CI234034.1|CI234034
EST:     AGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: AGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
EST: gi|33793662|gb|CF322715.1|CF322715
EST:     CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCC
genomic: CTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCC
EST: gi|87013954|gb|CI271345.1|CI271345
EST:     GGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAG                         ATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT
genomic: GGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGAT

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: 40 (upstream exon), 39 (downstream exon)
Score: 3

AGAAGTATTCCTGAACATCGCAAAGCAGGCAGAACTGGAGAGCTCTACTGCTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttcct ... ggcaatgcagATACCAAAGGGGGCTCGTTTTGTCGGAATTCCCGGAACCGAGTCGGAGGATCACCCAAGAGGCGTGATGGTTGAAGTTTACTGGGATCAAGATGACAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGTATTCCTGAACATCGCAAAGCAGGCAGAACTGGAGAGCTCTACTGCTGAAGGCACCCTGGTTACTCTGAACCTATCATCAGGTTCATCTATTCAGgtttgttccttagtacccctaagaacaatgctgcaatattggacatgaaaaggataatctcactgctatgtagagaacttctgtacagcagcaacagtac

- - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG