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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttacaagtttatttctattgtttgtctcttatgtagaaattgaactttaatcatatggtgactgcag

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 7
TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagtta-----caagtttattt-ctattgtttgtctcttatgtagaaattgaactttaatcat-atggtgactgcag
|||||||||||| || |||||||||||||| ||||||||||||||||||||||| || |||||||| ||||| |||||||| |||||||||||||| |||||| || |      |   |||  | | |||  || | | || ||||||||   | |||| ||| | ||  | |||||||
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaatctttacacttacatacaattagtttttttttttgtagaaac-aatctttgatctttatttttactgcag

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 22
TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca------agtttatttctattgtttgtctcttatgtagaaattgaactttaatcat-atggtgactgcag
|||||||||||| || |||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| |||||| || |        |||||  | | || |||  | | || | ||||||   | |||| ||| | ||  | |||||||
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaatctttacagtttcatacaatagtt--ttttttttctagaaac-aatctttgatctttatttttactgcag

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 21
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 20
TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca------------agtttatttctattgtttgtctc--ttatgtagaaattgaactttaatcatatggtgactgcag-----------------------------------------------
|||||| || || | |||| | ||  | || || || || || ||||| |||||||| || ||||||||| | ||| |||||||||||||||| || ||||| |  | |             ||| ||||| |||| |||||     | || | |  |      |||  |  | |||| | |                                                   
TGAAGATGCCGTGCCTTGCATAGCGCTCTCTAAAAACGACTCTTATGTGATGTCTGCGTCCGGAGGGAAAGTTTCTTTGTTCAACATGATGACATTCAAGgtaaagtccgcgaatcatgaggagtctattt-tattctttgttctaataatatggtgagaagcgttttgtt-tttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgactcag

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 21
lower sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 20
TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttacaagtttatttctattgtttgtctcttatgtagaaattgaactttaatcatatggtgactgcag
 ||||||||||| | |||| |||| |||||||||||||| || || || ||||| || || ||||| ||| | ||||| || || ||||||||||| |||||    | ||  ||| |   | |||   |       ||||  || |   |  |   ||              
GGAAGAAGCTGTGCCTTGCATTGCCTTGTCAAAGAATGACTCTTACGTGATGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgta---tgcacatttttccttcttgaccg------gtgtaagaacttg-ccatgtccag-------------

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|88348934|gb|CI653978.1|CI653978
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58658403|gb|CK047083.1|CK047083
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|88344056|gb|CI638791.1|CI638791
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58657128|gb|CK045808.1|CK045808
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58677432|gb|CK066119.1|CK066119
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58655231|gb|CK043911.1|CK043911
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58691548|gb|CK080235.1|CK080235
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58594272|gb|CF992580.1|CF992580
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58658854|gb|CK047534.1|CK047534
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58657970|gb|CK046650.1|CK046650
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTAGGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58656462|gb|CK045142.1|CK045142
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|88573729|gb|CI665498.1|CI665498
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|29680680|gb|CB676955.1|CB676955
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|163919897|gb|EG714407.1|EG714407
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAAC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAAC
EST: gi|58689471|gb|CK078158.1|CK078158
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58694923|gb|CK083610.1|CK083610
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|29673860|gb|CB670135.1|CB670135
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC

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), 71 (downstream exon)
Score: 83

TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttacaagtttatttctattgtttgtctcttatgtagaaattgaactttaatcatatggtgactgcag

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