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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctatttcatcaaatatagtgttagcttgctaaacagctgtaaaacatgcaccaaaacatcttattctttcaaagattaacttaacaagaactggga...

Basic information

species Oryza sativa
transcript LOC_Os01g07100.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07100.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G048804_T02 (Zea mays), 5'ss of exon 10
GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtag--ctatttcatcaaatatagtgttagcttgctaa--acagctgtaaaacatgcaccaaaacatcttattctttcaaagattaacttaacaagaactggga-----
 || || |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||  ||  |||| ||| |||||||||  || |||| ||||||||  ||||   | | |||  | | ||||  | |||| |        | | ||     | | ||| |   |   || |||||| |     
ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgtttc-tcaaatattttgttgcttcgttaagaatatctgtttagcatgaa--------tttgataggaaccaggataatagttttaaaaactggaaaaaat

upper sequence: LOC_Os01g07100.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G048804_T01 (Zea mays), 5'ss of exon 1
---------------GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtag--ctatttcatcaaatatagtgttagcttgctaa--acagctgtaaaacatgcaccaaaacatcttattctttcaaagattaacttaacaagaactggga-----
                || || |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||  ||  |||| ||| |||||||||  || |||| ||||||||  ||||   | | |||  | | ||||  | |||| |        | | ||     | | ||| |   |   || |||||| |     
TGACGCTGTTTACAGACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgtttc-tcaaatattttgttgcttcgttaagaatatctgtttagcatgaa--------tttgataggaaccaggataatagttttaaaaactggaaaaaat
















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|86503745|gb|CI146378.1|CI146378
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|88903452|gb|CI088990.1|CI088990
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|86419758|gb|CI054559.1|CI054559
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|58679649|gb|CK068336.1|CK068336
EST:     TGCGGCAGAAGTACAAGACAAGTACCGATCGCGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|87020089|gb|CI277821.1|CI277821
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|218478384|gb|FG957616.1|FG957616
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCGCGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|88269066|gb|CI380364.1|CI380364
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|88828968|gb|CI073838.1|CI073838
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|86872283|gb|CI323733.1|CI323733
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCCCAAAATTTTATGGAATAGCGGAGCCAGAGCGC
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATA-CGGAGCCAGAGCGC
EST: gi|88228931|gb|CI226782.1|CI226782
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|88266959|gb|CI378894.1|CI378894
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|88253480|gb|CI352106.1|CI352106
EST:     ACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: ACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|88476062|gb|CI413333.1|CI413333
EST:     CAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
genomic: CAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCT
EST: gi|86499373|gb|CI142006.1|CI142006
EST:     TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG                         TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCCAGAGCGC
genomic: TGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCC-AGAGCGC

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: 58 (upstream exon), 73 (downstream exon)
Score: 14

GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctattt ... tgggtttcagTTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtagctatttcatcaaatatagtgttagcttgctaaacagctgtaaaacatgcaccaaaacatcttattctttcaaagattaacttaacaagaactggga

- - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG