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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACTCAGTAGAGGATGATGTTGTCATGAAGCTATGGCGCCCTACCATGAAGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgtattcggagtaataaagttgctaaactgctgattgctttttcttttcgttcaaagcagaacccattgagttcttggcttctataaatttgcatttactgttaaactcgcatagtcaccacccagtccttttaaggcttatgctttagtactgacctgaagttactatgattatag

Basic information

species Oryza sativa
transcript LOC_Os01g66940.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G086845_T01 (Zea mays), 5'ss of exon 2
TGACTCAGTAGAGGATGATGTTGTCATGAAGCTATGGCGCCCTACCATGAAGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgtattcggagtaataaagttgctaaactgctgattgctttttcttttcgttcaaagcagaacccattgagttcttggcttctataaatttgcatttactgttaaactcg---catagtcaccacccagtccttttaaggcttatgctttagtactgacctgaagttactatgattatag
 ||||| || ||||| ||||||||||||||||| ||||| |||||||||||||| ||||| |||||||||||||||||||| ||||||||||||||||||||| |||  ||      |   |  | ||| |  ||    ||     |   || | | |       |||| | || ||    |         | | |   | ||  ||  | ||| |      ||     || |||   ||| ||      || ||   | | |                       
CGACTCGGTGGAGGACGATGTTGTCATGAAGCTGTGGCGGCCTACCATGAAGCTGCTCCTAGTGACTCTTGGAGATCAAGGGTGCAAGTACTATGCCAGGgtatgcttcata-actttttgattgctgccatcctatgaatgaaaatgggttattgat-------gaacacttttagcatatataactcgcacactgtgacttggtggaagacttgatgtgcagctgagactcagaagtttaaatatgcttgattggttgcag-----------------------

upper sequence: LOC_Os01g66940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 2
TGACTCAGTAGAGGATGATGTTGTCATGAAGCTATGGCGCCCTACCATGAAGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgtattcggagtaataaagttgctaaactgctgattgctttttcttttcgttcaaagcagaacccattgagttcttggcttctataaatttgcatttactgttaaactcgcatagtcaccacccagtccttttaaggcttatgct-ttagtactgacctgaagttactat----gattatag
  ||||||| ||||| ||||||||||||||||| ||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||||||| |||||||| ||| ||||     |   |  | ||||   ||   ||     | |  | ||  | | ||     |  ||| |  | |||   ||     || || || | | |||      |  ||    | |   || |  |||||     | |||   |   ||| ||      |||||||    ||||  ||
CAACTCAGTGGAGGACGATGTTGTCATGAAGCTGTGGCGACCTACCATGAAGCTGCTCCTGGTGACTCTTGGAGATCAAGGATGCAAGTACTATACCAGGgtatgctttattttatttttgattgctgctgtcctatggaaa---tgtgttgttgatgctaaat---attcatgggctgcttatatt----gaactttcact-agtgtcttggccaaattcaaagcgtacactttttttagcatatctgcagctgaaactcacacacgtttactatacttgattgcag
















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|88989124|gb|CI042237.1|CI042237
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|8857953|gb|AU095271.1|AU095271
EST:     ATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: ATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|86487292|gb|CI129925.1|CI129925
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGACCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|29681027|gb|CB677302.1|CB677302
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|86855291|gb|CI265217.1|CI265217
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|88243805|gb|CI242927.1|CI242927
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GGTTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|38475447|gb|CF959580.1|CF959580
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCA
EST: gi|29658300|gb|CB654575.1|CB654575
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|88241712|gb|CI241561.1|CI241561
EST:     GCTCCTCCTTGTGACTCTTGGAGATCATAGGATGCAAGTACTATGCCAGG                         GATTTCCTCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACTACA
genomic: GCTCCTCCTTGTGACTCTTGGAGATCA-AGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|15856845|gb|BI809657.1|BI809657
EST:     AGGATGCAAGTACTATGCCA-G                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATAC-ACA
genomic: AGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|58686862|gb|CK075549.1|CK075549
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|87029122|gb|CI276390.1|CI276390
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|86426341|gb|CI071438.1|CI071438
EST:     CAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: CAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|88244160|gb|CI243282.1|CI243282
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|86260900|gb|CI066575.1|CI066575
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGGGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
EST: gi|89193879|gb|CI018197.1|CI018197
EST:     AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGG                         GATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA
genomic: AGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACA

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: 72 (upstream exon), 75 (downstream exon)
Score: 57

TGACTCAGTAGAGGATGATGTTGTCATGAAGCTATGGCGCCCTACCATGAAGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgta ... atgattatagGATTTCCGCGGAGCTGTCCCATCCTACAAAGTACAGCAAGTTGATACAACAGGTGCAGGTGATGCGTTTGTTGGTGCTCTGCTGCGAAGAATTGTCCAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACTCAGTAGAGGATGATGTTGTCATGAAGCTATGGCGCCCTACCATGAAGCTCCTCCTTGTGACTCTTGGAGATCAAGGATGCAAGTACTATGCCAGGgtaagctgtattcggagtaataaagttgctaaactgctgattgctttttcttttcgttcaaagcagaacccattgagttcttggcttctataaatttgcatttactgttaaactcgcatagtcaccacccagtccttttaaggcttatgctttagtactgacctgaagttactatgattatag

- - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG