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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattatgttatgattttagttctttcaatactctgatgatgtgcaactccagcttttcttgtatgagacaacatttttactgtctgttctctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAAGGAAGAGGAGGCAGCAGCCGCAGCACCCGCAATGGGTGGCATGGGCGGG

Basic information

species Oryza sativa
transcript LOC_Os03g04970.1
intron # 17
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|88518524|gb|CI446178.1|CI446178
EST:     CAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: CAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|86536823|gb|CI177029.1|CI177029
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|38481227|gb|CF965316.1|CF965316
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88479347|gb|CI416618.1|CI416618
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88263413|gb|CI367187.1|CI367187
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|89192064|gb|CI393421.1|CI393421
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88252372|gb|CI350800.1|CI350800
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TTTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88224758|gb|CI224607.1|CI224607
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88446911|gb|CI528954.1|CI528954
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTTTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|86837997|gb|CI343294.1|CI343294
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|86493378|gb|CI136011.1|CI136011
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88518653|gb|CI446307.1|CI446307
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTTTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88455316|gb|CI519337.1|CI519337
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTTTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88506713|gb|CI434219.1|CI434219
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88487337|gb|CI424608.1|CI424608
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88502636|gb|CI430142.1|CI430142
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88481324|gb|CI418595.1|CI418595
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88269636|gb|CI380934.1|CI380934
EST:     TCATTGACCCACTAAAAGTTATCAAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: TCATTGACCCACTAAAAGTTATC-AGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88903313|gb|CI088851.1|CI088851
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|86536911|gb|CI177117.1|CI177117
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88483826|gb|CI421097.1|CI421097
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88842319|gb|CI081575.1|CI081575
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
EST: gi|88845406|gb|CI084331.1|CI084331
EST:     ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG                         TGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA
genomic: ATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAA

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: 25 (upstream exon), 20 (downstream exon)
Score: 1

GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAGgtactcttcc ... tctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAAGGAAGAGGAGGCAGCAGCCGCAGCACCCGCAATGGGTGGCATGGGCGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactccagcttttcttgtatgagacaacatttttactgtctgttctctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAAGGAAGAGGAGGCAGCAGCCGCAGCACCCGCAATGGGTGGCATGGGCGGG
                                      tctgttctct  CT-rich tract
                         aacattttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattatgttatgattttagttctttcaatactctgatgatgtgcaactccagcttttcttgtatgagacaacatttttactgtctgttctctattgcagTGTGTCCTCTCTAATGACTACCACAGAATCTATTATTGTTGAGATCCCCAAGGAAGAGGAGGCAGCAGCCGCAGCACCCGCAATGGGTGGCATGGGCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - tgttatg
- - - - - - - - - - - - - - - - -ctgatga
- - - - - - - - - - - - - - - - - - - - tgtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtctg