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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttatttttcctgtaaactttcagtatgcatttatcaatgtgttcttaccaggtttgactttgagttttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os08g07960.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 3
GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttatttttcctgta-aactttcagtatgcatttatcaatgtgttctt----accagg----------tttgactttgagttttgtgcag---
 ||||||| || ||||||||||| || || |||||||| ||||| || ||||| || || || |||||||| ||||||||||||||||||  |||  || | ||||  ||  | ||||  || ||| | | |||| | |     ||| ||          |||| |||||  ||||||  |    
ATACTGCCGAACCCAGGTGACTCTGTCTCCAGCCTCAGCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgcttatgctgtgtaatctgcagttggcctttgtaactgtgatgtatggaacccggattgtttggctttggctttgtattttgtctaccag
















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|88394469|gb|CI605810.1|CI605810
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|33793654|gb|CF322711.1|CF322711
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88451540|gb|CI565593.1|CI565593
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88357567|gb|CI623621.1|CI623621
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGTTTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|29615879|gb|CB620891.1|CB620891
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGGGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88356897|gb|CI620785.1|CI620785
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88399681|gb|CI583415.1|CI583415
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88314161|gb|CI602493.1|CI602493
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCACAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|33795033|gb|CF323392.1|CF323392
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|29681300|gb|CB677575.1|CB677575
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88397869|gb|CI583187.1|CI583187
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTA
EST: gi|88417412|gb|CI579073.1|CI579073
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|218492102|gb|FG950663.1|FG950663
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88394449|gb|CI605790.1|CI605790
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|58598341|gb|CK008869.1|CK008869
EST:     TTTAGCCCAGAGAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: TTTAGCCCA-A-AGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|10794894|gb|AU108860.1|AU108860
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCANCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|25799251|gb|CA755212.1|CA755212
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88417428|gb|CI579089.1|CI579089
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA

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: 65 (upstream exon), 75 (downstream exon)
Score: 24

GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttatttttcctgtaaactttcagtatgcatttatcaatgtgttcttaccaggtttgactttgagttttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG