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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAAGTACATGAAGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagttttacattgcactgtacatatcatgtgttgttcctgtgcttcctagttaacacgtacatcttttattacag

Basic information

species Oryza sativa
transcript LOC_Os02g47440.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 5
AGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAAGTACATGAAGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagt-tttacattgcactgtacatatcatgtgttgttcctgtgcttcctagttaacacgtacatc-ttttattacag
||||||||||| ||||||||||| ||||| ||||||||||||||||||||||  || || ||||||||||| |||||||||   |||||| | | ||||||||||| ||||||||| | ||| |||||  |||  |  |  |  ||||| ||| ||||  |||||      | || |||
AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtctttacattgtattgtgcatatgctgtcctagtttttagcttcttagctaacgtgtacactgccctgttccag
















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|86500468|gb|CI143101.1|CI143101
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|58606351|gb|CK034384.1|CK034384
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCGGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|29638446|gb|CB643455.1|CB643455
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|86505518|gb|CI148151.1|CI148151
EST:     TAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACCATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: TAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|29646264|gb|CB651271.1|CB651271
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|25806896|gb|CA762857.1|CA762857
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|58667527|gb|CK056213.1|CK056213
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|86421015|gb|CI057004.1|CI057004
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACCAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA

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: 50 (upstream exon), 72 (downstream exon)
Score: 32

AGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAAGTACATGAAGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAAAGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAAGTACATGAAGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagttttacattgcactgtacatatcatgtgttgttcctgtgcttcctagttaacacgtacatcttttattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG