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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggacgtgtgcgccattgctgcccgctctgatgtgtttcttgcagccttgatctgatgatggtacgctcgctctgagtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTCCGTGGCTGATGCAGCGGTCGTCTGCACTGATCCACAGAAGAACCCCATC

Basic information

species Oryza sativa
transcript LOC_Os04g47580.1
intron # 3
splice site 3'
intron type U2

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|88401846|gb|CI591173.1|CI591173
EST:     AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG                         GAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
genomic: AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAGgttaggacgt ... agtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
EST: gi|58661771|gb|CK050451.1|CK050451
EST:     AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG                         GAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
genomic: AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAGgttaggacgt ... agtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
EST: gi|58658155|gb|CK046835.1|CK046835
EST:     AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG                         GAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
genomic: AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAGgttaggacgt ... agtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
EST: gi|86831971|gb|CI305197.1|CI305197
EST:     AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG                         GAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
genomic: AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAGgttaggacgt ... agtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
EST: gi|88406938|gb|CI578466.1|CI578466
EST:     AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG                         GAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTTGACCATCAGGTTT
genomic: AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAGgttaggacgt ... agtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTT-GACCATCAGGTTT
EST: gi|58672181|gb|CK060867.1|CK060867
EST:     AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG                         GAATTTCGCGGACTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
genomic: AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAGgttaggacgt ... agtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTC
EST: gi|88694046|gb|CI738084.1|CI738084
EST:     AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG                         GAATTTCGCGGCCTCCTTG
genomic: AAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAGgttaggacgt ... agtgatccagGAATTTCGCGGCCTCCTTG

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), 73 (downstream exon)
Score: 16

GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAGgttaggacgt ... agtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTCCGTGGCTGATGCAGCGGTCGTCTGCACTGATCCACAGAAGAACCCCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgtttcttgcagccttgatctgatgatggtacgctcgctctgagtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTCCGTGGCTGATGCAGCGGTCGTCTGCACTGATCCACAGAAGAACCCCATC
                    atctgat  putative branch site (score: 16)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggacgtgtgcgccattgctgcccgctctgatgtgtttcttgcagccttgatctgatgatggtacgctcgctctgagtgatccagGAATTTCGCGGCCTCCTTGACGCGAAAAGAACAGCTTGACCATCAGGTTTCCGTGGCTGATGCAGCGGTCGTCTGCACTGATCCACAGAAGAACCCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC